Starting phenix.real_space_refine on Fri Mar 6 07:09:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o72_0638/03_2026/6o72_0638.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Na 8 4.78 5 C 18776 2.51 5 N 4604 2.21 5 O 5028 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28592 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "B" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "D" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 140 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 3, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 7.23, per 1000 atoms: 0.25 Number of scatterers: 28592 At special positions: 0 Unit cell: (128.139, 128.139, 145.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 148 16.00 P 4 15.00 Na 8 11.00 F 24 9.00 O 5028 8.00 N 4604 7.00 C 18776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.4 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 8 sheets defined 70.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 724 through 749 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP A 787 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET A 849 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 879 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'A' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1014 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1089 through 1094' Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.709A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 358' Processing helix chain 'B' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 393 through 409 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.676A pdb=" N ASN B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.519A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.797A pdb=" N LYS B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY B 697 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 724 through 749 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP B 787 " --> pdb=" O TYR B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 806 removed outlier: 3.805A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET B 849 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 879 Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.594A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 994 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 Processing helix chain 'B' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B1014 " --> pdb=" O TYR B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1087 Processing helix chain 'B' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1089 through 1094' Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.711A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 361 through 374 removed outlier: 4.092A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 393 through 409 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.579A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.889A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY C 697 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 722 Processing helix chain 'C' and resid 724 through 749 Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP C 787 " --> pdb=" O TYR C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 799 " --> pdb=" O LEU C 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET C 849 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 879 Processing helix chain 'C' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.281A pdb=" N TYR C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS C 951 " --> pdb=" O ILE C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.732A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 995 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1005 Processing helix chain 'C' and resid 1006 through 1014 removed outlier: 4.324A pdb=" N PHE C1012 " --> pdb=" O PHE C1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C1014 " --> pdb=" O TYR C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1059 removed outlier: 3.529A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG C1071 " --> pdb=" O GLU C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1087 Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1089 through 1094' Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 4.185A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 358' Processing helix chain 'D' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 393 through 409 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN D 501 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY D 697 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 722 Processing helix chain 'D' and resid 724 through 749 Processing helix chain 'D' and resid 756 through 766 Processing helix chain 'D' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP D 787 " --> pdb=" O TYR D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 799 " --> pdb=" O LEU D 795 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 806 " --> pdb=" O ALA D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 842 " --> pdb=" O THR D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET D 849 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 879 Processing helix chain 'D' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR D 898 " --> pdb=" O ILE D 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS D 951 " --> pdb=" O ILE D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 994 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 995 " --> pdb=" O LEU D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1005 Processing helix chain 'D' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE D1012 " --> pdb=" O PHE D1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG D1071 " --> pdb=" O GLU D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1087 Processing helix chain 'D' and resid 1089 through 1094 removed outlier: 3.581A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1089 through 1094' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 170 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 205 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 172 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 292 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE B 170 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 205 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 172 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 292 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE C 170 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 205 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 172 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 292 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 170 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 205 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 172 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 292 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 4320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.69 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4480 1.31 - 1.44: 8218 1.44 - 1.56: 16246 1.56 - 1.69: 48 1.69 - 1.82: 244 Bond restraints: 29236 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C19 T14 C1305 " pdb=" N20 T14 C1305 " ideal model delta sigma weight residual 1.274 1.446 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 29231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 39117 4.69 - 9.38: 335 9.38 - 14.06: 48 14.06 - 18.75: 12 18.75 - 23.44: 4 Bond angle restraints: 39516 Sorted by residual: angle pdb=" C PHE B1003 " pdb=" N PRO B1004 " pdb=" CA PRO B1004 " ideal model delta sigma weight residual 119.87 108.20 11.67 1.04e+00 9.25e-01 1.26e+02 angle pdb=" C PHE A1003 " pdb=" N PRO A1004 " pdb=" CA PRO A1004 " ideal model delta sigma weight residual 119.87 108.22 11.65 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE C1003 " pdb=" N PRO C1004 " pdb=" CA PRO C1004 " ideal model delta sigma weight residual 119.87 108.23 11.64 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE D1003 " pdb=" N PRO D1004 " pdb=" CA PRO D1004 " ideal model delta sigma weight residual 119.87 108.25 11.62 1.04e+00 9.25e-01 1.25e+02 angle pdb=" N HIS B 412 " pdb=" CA HIS B 412 " pdb=" C HIS B 412 " ideal model delta sigma weight residual 112.92 99.93 12.99 1.23e+00 6.61e-01 1.12e+02 ... (remaining 39511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 16775 31.24 - 62.47: 637 62.47 - 93.71: 56 93.71 - 124.95: 4 124.95 - 156.19: 4 Dihedral angle restraints: 17476 sinusoidal: 7408 harmonic: 10068 Sorted by residual: dihedral pdb=" CA SER D 638 " pdb=" C SER D 638 " pdb=" N CYS D 639 " pdb=" CA CYS D 639 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER A 638 " pdb=" C SER A 638 " pdb=" N CYS A 639 " pdb=" CA CYS A 639 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N CYS C 639 " pdb=" CA CYS C 639 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4117 0.101 - 0.202: 255 0.202 - 0.304: 19 0.304 - 0.405: 5 0.405 - 0.506: 4 Chirality restraints: 4400 Sorted by residual: chirality pdb=" CBI Y01 B1301 " pdb=" CAU Y01 B1301 " pdb=" CBE Y01 B1301 " pdb=" CBG Y01 B1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4397 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 947 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 947 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 947 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 948 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.047 5.00e-02 4.00e+02 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 293 2.63 - 3.20: 24432 3.20 - 3.76: 44890 3.76 - 4.33: 64913 4.33 - 4.90: 101723 Nonbonded interactions: 236251 Sorted by model distance: nonbonded pdb=" O TYR D 286 " pdb=" O GLY D 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR C 286 " pdb=" O GLY C 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR A 286 " pdb=" O GLY A 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR B 286 " pdb=" O GLY B 288 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR B 115 " pdb=" OD1 ASP B 116 " model vdw 2.291 3.040 ... (remaining 236246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 96 through 1303 or resid 1306)) selection = (chain 'B' and (resid 96 through 1303 or resid 1306)) selection = (chain 'C' and (resid 96 through 1303 or resid 1306)) selection = (chain 'D' and (resid 96 through 1303 or resid 1306)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 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: 0.050 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.357 29240 Z= 0.463 Angle : 1.197 23.439 39516 Z= 0.617 Chirality : 0.059 0.506 4400 Planarity : 0.007 0.084 4816 Dihedral : 16.340 156.185 10924 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.25 (0.08), residues: 3336 helix: -4.15 (0.05), residues: 2240 sheet: -2.60 (0.35), residues: 176 loop : -3.67 (0.15), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 238 TYR 0.015 0.002 TYR C 286 PHE 0.033 0.002 PHE D 700 TRP 0.023 0.002 TRP D 984 HIS 0.005 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00938 (29236) covalent geometry : angle 1.19729 (39516) hydrogen bonds : bond 0.27747 ( 1448) hydrogen bonds : angle 10.08440 ( 4320) Misc. bond : bond 0.10138 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 837 time to evaluate : 1.090 Fit side-chains REVERT: A 161 TYR cc_start: 0.8111 (t80) cc_final: 0.7626 (t80) REVERT: A 281 ILE cc_start: 0.8487 (tt) cc_final: 0.7496 (tt) REVERT: A 422 LYS cc_start: 0.8770 (mttt) cc_final: 0.8382 (mttp) REVERT: A 426 GLU cc_start: 0.7664 (tp30) cc_final: 0.7100 (tp30) REVERT: A 440 ASN cc_start: 0.7643 (m-40) cc_final: 0.7405 (m110) REVERT: A 565 LYS cc_start: 0.8647 (ttmm) cc_final: 0.8387 (tttp) REVERT: A 611 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 734 ILE cc_start: 0.9053 (mt) cc_final: 0.8812 (mm) REVERT: A 772 ASP cc_start: 0.8093 (t0) cc_final: 0.7520 (t0) REVERT: B 281 ILE cc_start: 0.8545 (tt) cc_final: 0.7525 (tt) REVERT: B 426 GLU cc_start: 0.7839 (tp30) cc_final: 0.7219 (tp30) REVERT: B 440 ASN cc_start: 0.7731 (m-40) cc_final: 0.7426 (m110) REVERT: B 604 GLU cc_start: 0.7933 (pt0) cc_final: 0.7700 (pt0) REVERT: B 611 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 793 ASP cc_start: 0.7906 (m-30) cc_final: 0.7694 (m-30) REVERT: B 1001 ILE cc_start: 0.8668 (mt) cc_final: 0.8384 (pp) REVERT: C 161 TYR cc_start: 0.8148 (t80) cc_final: 0.7947 (t80) REVERT: C 211 ILE cc_start: 0.8118 (pt) cc_final: 0.7914 (pp) REVERT: C 281 ILE cc_start: 0.8523 (tt) cc_final: 0.7507 (tt) REVERT: C 426 GLU cc_start: 0.7821 (tp30) cc_final: 0.7221 (tp30) REVERT: C 440 ASN cc_start: 0.7705 (m-40) cc_final: 0.7419 (m110) REVERT: C 596 LYS cc_start: 0.8461 (mttp) cc_final: 0.8245 (mttp) REVERT: C 604 GLU cc_start: 0.7931 (pt0) cc_final: 0.7699 (pt0) REVERT: C 611 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 793 ASP cc_start: 0.7906 (m-30) cc_final: 0.7698 (m-30) REVERT: D 211 ILE cc_start: 0.8119 (pt) cc_final: 0.7904 (pp) REVERT: D 281 ILE cc_start: 0.8576 (tt) cc_final: 0.7616 (tt) REVERT: D 422 LYS cc_start: 0.8708 (mttt) cc_final: 0.8283 (mttp) REVERT: D 426 GLU cc_start: 0.7853 (tp30) cc_final: 0.7236 (tp30) REVERT: D 440 ASN cc_start: 0.7790 (m-40) cc_final: 0.7496 (m110) REVERT: D 604 GLU cc_start: 0.7940 (pt0) cc_final: 0.7710 (pt0) REVERT: D 611 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 0 outliers final: 2 residues processed: 837 average time/residue: 0.5763 time to fit residues: 570.2467 Evaluate side-chains 603 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 601 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain D residue 276 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 248 HIS A 297 GLN A 429 GLN A 491 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 987 GLN A1070 HIS B 145 ASN B 248 HIS B 297 GLN B 418 ASN B 429 GLN B 491 ASN B 851 GLN B 987 GLN B1070 HIS C 145 ASN C 248 HIS C 297 GLN C 418 ASN C 429 GLN C 491 ASN C 851 GLN C 987 GLN C1070 HIS D 145 ASN D 248 HIS D 297 GLN D 429 GLN D 491 ASN D 851 GLN D 987 GLN D1070 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.174266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131970 restraints weight = 35988.644| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.31 r_work: 0.3344 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29240 Z= 0.148 Angle : 0.697 14.646 39516 Z= 0.356 Chirality : 0.043 0.210 4400 Planarity : 0.005 0.058 4816 Dihedral : 11.275 143.092 4260 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.39 % Allowed : 17.71 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.43 (0.12), residues: 3336 helix: -1.77 (0.09), residues: 2264 sheet: -2.47 (0.36), residues: 176 loop : -3.10 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 998 TYR 0.038 0.002 TYR B 286 PHE 0.018 0.001 PHE C 751 TRP 0.014 0.002 TRP C 867 HIS 0.007 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00339 (29236) covalent geometry : angle 0.69677 (39516) hydrogen bonds : bond 0.03983 ( 1448) hydrogen bonds : angle 4.82424 ( 4320) Misc. bond : bond 0.00228 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 691 time to evaluate : 1.020 Fit side-chains REVERT: A 161 TYR cc_start: 0.8444 (t80) cc_final: 0.8198 (t80) REVERT: A 274 LYS cc_start: 0.8426 (ttpt) cc_final: 0.7851 (tppt) REVERT: A 328 ASP cc_start: 0.7697 (m-30) cc_final: 0.7481 (m-30) REVERT: A 512 LEU cc_start: 0.8920 (mt) cc_final: 0.8701 (tp) REVERT: A 734 ILE cc_start: 0.9111 (mt) cc_final: 0.8893 (mm) REVERT: A 772 ASP cc_start: 0.8414 (t0) cc_final: 0.7840 (t0) REVERT: A 784 TYR cc_start: 0.6670 (t80) cc_final: 0.6429 (t80) REVERT: A 793 ASP cc_start: 0.8190 (m-30) cc_final: 0.7920 (m-30) REVERT: A 852 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8115 (ttm170) REVERT: A 879 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6788 (pp) REVERT: B 161 TYR cc_start: 0.8513 (t80) cc_final: 0.8286 (t80) REVERT: B 190 ASN cc_start: 0.8511 (t0) cc_final: 0.8301 (OUTLIER) REVERT: B 328 ASP cc_start: 0.7576 (m-30) cc_final: 0.7363 (m-30) REVERT: B 386 LYS cc_start: 0.7977 (tppt) cc_final: 0.7681 (tppt) REVERT: B 498 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8439 (tttm) REVERT: B 512 LEU cc_start: 0.8968 (mt) cc_final: 0.8753 (tp) REVERT: B 772 ASP cc_start: 0.8419 (t0) cc_final: 0.7836 (t0) REVERT: B 776 GLN cc_start: 0.6777 (mp10) cc_final: 0.6551 (mp10) REVERT: B 793 ASP cc_start: 0.8238 (m-30) cc_final: 0.7969 (m-30) REVERT: B 852 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: B 879 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6780 (pp) REVERT: B 984 TRP cc_start: 0.7712 (t60) cc_final: 0.7409 (t60) REVERT: C 121 TYR cc_start: 0.8092 (t80) cc_final: 0.7846 (t80) REVERT: C 161 TYR cc_start: 0.8498 (t80) cc_final: 0.8253 (t80) REVERT: C 164 GLN cc_start: 0.8194 (tp40) cc_final: 0.7905 (tp40) REVERT: C 211 ILE cc_start: 0.8093 (pt) cc_final: 0.7816 (pp) REVERT: C 512 LEU cc_start: 0.8970 (mt) cc_final: 0.8757 (tp) REVERT: C 518 MET cc_start: 0.8710 (ttp) cc_final: 0.8497 (ptm) REVERT: C 596 LYS cc_start: 0.8585 (mttp) cc_final: 0.8303 (mttp) REVERT: C 672 GLN cc_start: 0.8642 (mt0) cc_final: 0.8334 (tp40) REVERT: C 763 TYR cc_start: 0.8791 (m-80) cc_final: 0.8558 (m-80) REVERT: C 772 ASP cc_start: 0.8179 (t0) cc_final: 0.7673 (t0) REVERT: C 793 ASP cc_start: 0.8189 (m-30) cc_final: 0.7954 (m-30) REVERT: C 879 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6877 (pp) REVERT: C 953 TYR cc_start: 0.8305 (m-80) cc_final: 0.8103 (m-80) REVERT: D 211 ILE cc_start: 0.8147 (pt) cc_final: 0.7889 (pp) REVERT: D 422 LYS cc_start: 0.8724 (mttt) cc_final: 0.8480 (mtmt) REVERT: D 512 LEU cc_start: 0.8974 (mt) cc_final: 0.8770 (tp) REVERT: D 772 ASP cc_start: 0.8281 (t0) cc_final: 0.7690 (t0) REVERT: D 852 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8172 (ttm170) REVERT: D 879 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6824 (pp) REVERT: D 993 GLN cc_start: 0.8429 (tt0) cc_final: 0.8059 (tp40) outliers start: 104 outliers final: 59 residues processed: 743 average time/residue: 0.5278 time to fit residues: 471.3549 Evaluate side-chains 652 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 587 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 852 ARG Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 817 SER Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 879 LEU Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 817 SER Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 316 optimal weight: 0.0970 chunk 253 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 418 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN C 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132012 restraints weight = 36073.131| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.31 r_work: 0.3349 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 29240 Z= 0.140 Angle : 0.639 13.227 39516 Z= 0.326 Chirality : 0.042 0.186 4400 Planarity : 0.004 0.049 4816 Dihedral : 10.638 131.285 4256 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.58 % Allowed : 21.71 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3336 helix: -0.61 (0.10), residues: 2276 sheet: -2.60 (0.35), residues: 176 loop : -2.77 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 998 TYR 0.035 0.002 TYR C 286 PHE 0.016 0.001 PHE A 703 TRP 0.015 0.001 TRP D 867 HIS 0.004 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00332 (29236) covalent geometry : angle 0.63943 (39516) hydrogen bonds : bond 0.03477 ( 1448) hydrogen bonds : angle 4.32537 ( 4320) Misc. bond : bond 0.00330 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 646 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 TYR cc_start: 0.8482 (t80) cc_final: 0.8232 (t80) REVERT: A 200 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 274 LYS cc_start: 0.8484 (ttpt) cc_final: 0.7862 (tppt) REVERT: A 328 ASP cc_start: 0.7432 (m-30) cc_final: 0.7175 (m-30) REVERT: A 374 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 501 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: A 565 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8722 (tttp) REVERT: A 776 GLN cc_start: 0.6772 (mp10) cc_final: 0.6551 (mp10) REVERT: A 784 TYR cc_start: 0.6769 (t80) cc_final: 0.6459 (t80) REVERT: A 793 ASP cc_start: 0.8164 (m-30) cc_final: 0.7925 (m-30) REVERT: A 879 LEU cc_start: 0.7226 (mm) cc_final: 0.6811 (pp) REVERT: B 328 ASP cc_start: 0.7439 (m-30) cc_final: 0.7231 (m-30) REVERT: B 371 TRP cc_start: 0.7342 (m100) cc_final: 0.6976 (m-10) REVERT: B 374 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 440 ASN cc_start: 0.7974 (m-40) cc_final: 0.7547 (m110) REVERT: B 512 LEU cc_start: 0.8978 (mt) cc_final: 0.8764 (tp) REVERT: B 565 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8765 (tttp) REVERT: B 772 ASP cc_start: 0.8417 (t0) cc_final: 0.7823 (t0) REVERT: B 793 ASP cc_start: 0.8127 (m-30) cc_final: 0.7901 (m-30) REVERT: C 161 TYR cc_start: 0.8544 (t80) cc_final: 0.8329 (t80) REVERT: C 200 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 211 ILE cc_start: 0.8058 (pt) cc_final: 0.7828 (pp) REVERT: C 371 TRP cc_start: 0.7343 (m100) cc_final: 0.7035 (m-10) REVERT: C 440 ASN cc_start: 0.7960 (m-40) cc_final: 0.7564 (m110) REVERT: C 512 LEU cc_start: 0.8995 (mt) cc_final: 0.8785 (tp) REVERT: C 565 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8642 (tttp) REVERT: C 596 LYS cc_start: 0.8639 (mttp) cc_final: 0.8377 (mttp) REVERT: C 676 GLU cc_start: 0.8460 (tp30) cc_final: 0.7954 (mp0) REVERT: C 793 ASP cc_start: 0.8165 (m-30) cc_final: 0.7950 (m-30) REVERT: C 1068 MET cc_start: 0.4420 (tpt) cc_final: 0.4138 (tpt) REVERT: D 211 ILE cc_start: 0.8093 (pt) cc_final: 0.7862 (pp) REVERT: D 274 LYS cc_start: 0.8439 (ttpt) cc_final: 0.7823 (tppt) REVERT: D 371 TRP cc_start: 0.7292 (m100) cc_final: 0.7027 (m-10) REVERT: D 440 ASN cc_start: 0.7938 (m-40) cc_final: 0.7540 (m110) REVERT: D 565 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8610 (tttp) REVERT: D 676 GLU cc_start: 0.8389 (tp30) cc_final: 0.7870 (mp0) REVERT: D 763 TYR cc_start: 0.8668 (m-80) cc_final: 0.8442 (m-80) REVERT: D 993 GLN cc_start: 0.8247 (tt0) cc_final: 0.8044 (mt0) outliers start: 110 outliers final: 58 residues processed: 686 average time/residue: 0.5290 time to fit residues: 434.7846 Evaluate side-chains 655 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 592 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 855 ILE Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 209 optimal weight: 1.9990 chunk 255 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 226 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 252 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN A 646 ASN A 993 GLN B 297 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128233 restraints weight = 36238.658| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.36 r_work: 0.3306 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29240 Z= 0.177 Angle : 0.644 12.343 39516 Z= 0.331 Chirality : 0.043 0.184 4400 Planarity : 0.004 0.063 4816 Dihedral : 10.300 119.360 4256 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.98 % Allowed : 21.81 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3336 helix: -0.18 (0.10), residues: 2308 sheet: -2.58 (0.35), residues: 176 loop : -2.61 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 998 TYR 0.034 0.002 TYR C 286 PHE 0.015 0.002 PHE C 514 TRP 0.017 0.002 TRP D 888 HIS 0.005 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00425 (29236) covalent geometry : angle 0.64417 (39516) hydrogen bonds : bond 0.03405 ( 1448) hydrogen bonds : angle 4.12404 ( 4320) Misc. bond : bond 0.00373 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 665 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 274 LYS cc_start: 0.8510 (ttpt) cc_final: 0.7906 (tppt) REVERT: A 374 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 426 GLU cc_start: 0.8500 (tp30) cc_final: 0.8116 (tp30) REVERT: A 440 ASN cc_start: 0.7887 (m-40) cc_final: 0.7478 (m110) REVERT: A 498 LYS cc_start: 0.8737 (tttm) cc_final: 0.8456 (tttm) REVERT: A 565 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8744 (tttp) REVERT: A 773 GLU cc_start: 0.8252 (tt0) cc_final: 0.8010 (tt0) REVERT: A 784 TYR cc_start: 0.6817 (t80) cc_final: 0.6615 (t80) REVERT: A 793 ASP cc_start: 0.8198 (m-30) cc_final: 0.7899 (m-30) REVERT: B 264 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.6977 (t) REVERT: B 274 LYS cc_start: 0.8600 (ttpt) cc_final: 0.7970 (tppt) REVERT: B 426 GLU cc_start: 0.8528 (tp30) cc_final: 0.8137 (tp30) REVERT: B 439 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7733 (t) REVERT: B 440 ASN cc_start: 0.7963 (m-40) cc_final: 0.7536 (m110) REVERT: B 481 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8526 (m) REVERT: B 565 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8724 (tttp) REVERT: B 676 GLU cc_start: 0.8486 (tp30) cc_final: 0.7977 (mp0) REVERT: B 749 MET cc_start: 0.8304 (mmm) cc_final: 0.8096 (mpp) REVERT: B 793 ASP cc_start: 0.8168 (m-30) cc_final: 0.7934 (m-30) REVERT: B 852 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8228 (ptp90) REVERT: B 985 LYS cc_start: 0.9099 (mttm) cc_final: 0.8845 (mttt) REVERT: C 208 TRP cc_start: 0.7472 (t-100) cc_final: 0.7026 (t60) REVERT: C 211 ILE cc_start: 0.8088 (pt) cc_final: 0.7843 (pp) REVERT: C 264 THR cc_start: 0.7376 (m) cc_final: 0.7091 (t) REVERT: C 274 LYS cc_start: 0.8494 (ttpt) cc_final: 0.7914 (tppt) REVERT: C 426 GLU cc_start: 0.8493 (tp30) cc_final: 0.8114 (tp30) REVERT: C 440 ASN cc_start: 0.7973 (m-40) cc_final: 0.7604 (m110) REVERT: C 481 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8409 (m) REVERT: C 676 GLU cc_start: 0.8465 (tp30) cc_final: 0.7977 (mp0) REVERT: C 763 TYR cc_start: 0.8668 (m-80) cc_final: 0.8453 (m-80) REVERT: C 784 TYR cc_start: 0.6966 (t80) cc_final: 0.6653 (t80) REVERT: C 985 LYS cc_start: 0.9114 (mttm) cc_final: 0.8856 (mttt) REVERT: D 208 TRP cc_start: 0.7500 (t-100) cc_final: 0.7068 (t60) REVERT: D 211 ILE cc_start: 0.8077 (pt) cc_final: 0.7832 (pp) REVERT: D 264 THR cc_start: 0.7291 (OUTLIER) cc_final: 0.7002 (t) REVERT: D 274 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7881 (tppt) REVERT: D 374 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: D 426 GLU cc_start: 0.8510 (tp30) cc_final: 0.8138 (tp30) REVERT: D 440 ASN cc_start: 0.7943 (m-40) cc_final: 0.7578 (m110) REVERT: D 565 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8696 (tttp) REVERT: D 676 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: D 784 TYR cc_start: 0.7134 (t80) cc_final: 0.6804 (t80) REVERT: D 790 ASN cc_start: 0.8285 (m-40) cc_final: 0.8074 (m-40) REVERT: D 852 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8171 (ptp90) REVERT: D 985 LYS cc_start: 0.9118 (mttm) cc_final: 0.8892 (mmtt) REVERT: D 993 GLN cc_start: 0.8393 (tt0) cc_final: 0.8170 (tt0) outliers start: 153 outliers final: 77 residues processed: 739 average time/residue: 0.5330 time to fit residues: 473.1541 Evaluate side-chains 675 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 589 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 852 ARG Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 326 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 169 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 308 ASN A 657 GLN A 993 GLN B 297 GLN B 501 GLN C 297 GLN C 501 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.172839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130020 restraints weight = 35958.098| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.36 r_work: 0.3325 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29240 Z= 0.143 Angle : 0.621 12.009 39516 Z= 0.316 Chirality : 0.042 0.193 4400 Planarity : 0.004 0.063 4816 Dihedral : 9.534 96.752 4256 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.72 % Allowed : 23.57 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3336 helix: 0.18 (0.11), residues: 2336 sheet: -2.50 (0.35), residues: 176 loop : -2.52 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 998 TYR 0.033 0.002 TYR B 286 PHE 0.015 0.001 PHE A1005 TRP 0.017 0.001 TRP A 888 HIS 0.004 0.001 HIS D 176 Details of bonding type rmsd covalent geometry : bond 0.00345 (29236) covalent geometry : angle 0.62099 (39516) hydrogen bonds : bond 0.03250 ( 1448) hydrogen bonds : angle 3.98244 ( 4320) Misc. bond : bond 0.00263 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 669 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6991 (t) REVERT: A 274 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7950 (tppt) REVERT: A 374 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: A 426 GLU cc_start: 0.8493 (tp30) cc_final: 0.8107 (tp30) REVERT: A 440 ASN cc_start: 0.7941 (m-40) cc_final: 0.7534 (m110) REVERT: A 498 LYS cc_start: 0.8749 (tttm) cc_final: 0.8519 (tttm) REVERT: A 565 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8746 (tttp) REVERT: A 779 MET cc_start: 0.7559 (ppp) cc_final: 0.7302 (pmm) REVERT: A 784 TYR cc_start: 0.6912 (t80) cc_final: 0.6465 (t80) REVERT: A 793 ASP cc_start: 0.8166 (m-30) cc_final: 0.7911 (m-30) REVERT: A 971 TYR cc_start: 0.8736 (p90) cc_final: 0.8340 (p90) REVERT: B 264 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.7042 (t) REVERT: B 274 LYS cc_start: 0.8601 (ttpt) cc_final: 0.7964 (tppt) REVERT: B 426 GLU cc_start: 0.8495 (tp30) cc_final: 0.8106 (tp30) REVERT: B 440 ASN cc_start: 0.7936 (m-40) cc_final: 0.7532 (m110) REVERT: B 565 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8728 (tttp) REVERT: B 676 GLU cc_start: 0.8414 (tp30) cc_final: 0.7974 (mp0) REVERT: B 773 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: B 784 TYR cc_start: 0.7354 (t80) cc_final: 0.7090 (t80) REVERT: B 793 ASP cc_start: 0.8152 (m-30) cc_final: 0.7812 (m-30) REVERT: B 852 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8020 (ptp90) REVERT: B 879 LEU cc_start: 0.7515 (mm) cc_final: 0.6865 (pp) REVERT: B 981 ASP cc_start: 0.8001 (t70) cc_final: 0.7743 (t0) REVERT: B 1068 MET cc_start: 0.5755 (tpt) cc_final: 0.5498 (tpt) REVERT: C 211 ILE cc_start: 0.8044 (pt) cc_final: 0.7786 (pp) REVERT: C 274 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7944 (tppt) REVERT: C 374 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: C 426 GLU cc_start: 0.8451 (tp30) cc_final: 0.8066 (tp30) REVERT: C 440 ASN cc_start: 0.7917 (m-40) cc_final: 0.7528 (m110) REVERT: C 565 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8731 (tttp) REVERT: C 676 GLU cc_start: 0.8482 (tp30) cc_final: 0.7998 (mp0) REVERT: C 763 TYR cc_start: 0.8680 (m-80) cc_final: 0.8432 (m-80) REVERT: C 784 TYR cc_start: 0.6842 (t80) cc_final: 0.6486 (t80) REVERT: C 793 ASP cc_start: 0.8175 (m-30) cc_final: 0.7938 (m-30) REVERT: C 879 LEU cc_start: 0.7534 (mm) cc_final: 0.6871 (pp) REVERT: C 981 ASP cc_start: 0.7989 (t70) cc_final: 0.7631 (t0) REVERT: C 1068 MET cc_start: 0.5707 (tpt) cc_final: 0.5417 (tpt) REVERT: D 211 ILE cc_start: 0.8069 (pt) cc_final: 0.7812 (pp) REVERT: D 233 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7258 (mtm) REVERT: D 274 LYS cc_start: 0.8599 (ttpt) cc_final: 0.7983 (tppt) REVERT: D 374 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: D 426 GLU cc_start: 0.8471 (tp30) cc_final: 0.8081 (tp30) REVERT: D 440 ASN cc_start: 0.7934 (m-40) cc_final: 0.7594 (m110) REVERT: D 565 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8731 (tttp) REVERT: D 676 GLU cc_start: 0.8436 (tp30) cc_final: 0.7953 (mp0) REVERT: D 763 TYR cc_start: 0.8599 (m-80) cc_final: 0.8395 (m-80) REVERT: D 879 LEU cc_start: 0.7503 (mm) cc_final: 0.6841 (pp) outliers start: 145 outliers final: 72 residues processed: 743 average time/residue: 0.5300 time to fit residues: 471.8280 Evaluate side-chains 674 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 595 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 672 GLN Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 849 MET Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 233 MET Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 517 LYS Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 127 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 993 GLN B 297 GLN C 297 GLN D 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126215 restraints weight = 36116.612| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.35 r_work: 0.3281 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29240 Z= 0.187 Angle : 0.666 11.265 39516 Z= 0.337 Chirality : 0.044 0.187 4400 Planarity : 0.004 0.054 4816 Dihedral : 9.508 86.996 4256 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.69 % Allowed : 24.48 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3336 helix: 0.30 (0.11), residues: 2312 sheet: -2.42 (0.36), residues: 176 loop : -2.42 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 998 TYR 0.031 0.002 TYR B 286 PHE 0.015 0.001 PHE A 514 TRP 0.017 0.002 TRP A 888 HIS 0.006 0.001 HIS C 176 Details of bonding type rmsd covalent geometry : bond 0.00452 (29236) covalent geometry : angle 0.66642 (39516) hydrogen bonds : bond 0.03371 ( 1448) hydrogen bonds : angle 3.98528 ( 4320) Misc. bond : bond 0.00440 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 622 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7013 (t) REVERT: A 274 LYS cc_start: 0.8608 (ttpt) cc_final: 0.7931 (tppt) REVERT: A 374 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: A 426 GLU cc_start: 0.8524 (tp30) cc_final: 0.8116 (tp30) REVERT: A 440 ASN cc_start: 0.7932 (m-40) cc_final: 0.7528 (m110) REVERT: A 498 LYS cc_start: 0.8773 (tttm) cc_final: 0.8492 (tttm) REVERT: A 784 TYR cc_start: 0.6978 (t80) cc_final: 0.6760 (t80) REVERT: A 971 TYR cc_start: 0.8827 (p90) cc_final: 0.8387 (p90) REVERT: B 164 GLN cc_start: 0.8607 (tp40) cc_final: 0.8375 (tp40) REVERT: B 274 LYS cc_start: 0.8617 (ttpt) cc_final: 0.7925 (tppt) REVERT: B 371 TRP cc_start: 0.7343 (m100) cc_final: 0.6888 (m-10) REVERT: B 426 GLU cc_start: 0.8524 (tp30) cc_final: 0.8128 (tp30) REVERT: B 440 ASN cc_start: 0.7972 (m-40) cc_final: 0.7566 (m110) REVERT: B 676 GLU cc_start: 0.8426 (tp30) cc_final: 0.7972 (mp0) REVERT: B 852 ARG cc_start: 0.8380 (ttm170) cc_final: 0.8076 (ptp90) REVERT: B 1068 MET cc_start: 0.5664 (tpt) cc_final: 0.5434 (tpt) REVERT: C 211 ILE cc_start: 0.8099 (pt) cc_final: 0.7820 (pp) REVERT: C 274 LYS cc_start: 0.8569 (ttpt) cc_final: 0.7863 (tppt) REVERT: C 374 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: C 426 GLU cc_start: 0.8516 (tp30) cc_final: 0.8121 (tp30) REVERT: C 440 ASN cc_start: 0.7876 (m-40) cc_final: 0.7474 (m110) REVERT: C 672 GLN cc_start: 0.8717 (mt0) cc_final: 0.8417 (tp40) REVERT: C 676 GLU cc_start: 0.8487 (tp30) cc_final: 0.7992 (mp0) REVERT: C 793 ASP cc_start: 0.8272 (m-30) cc_final: 0.8059 (m-30) REVERT: C 1068 MET cc_start: 0.5487 (tpt) cc_final: 0.5152 (tpt) REVERT: D 164 GLN cc_start: 0.8618 (tp40) cc_final: 0.8392 (tp40) REVERT: D 211 ILE cc_start: 0.8140 (pt) cc_final: 0.7869 (pp) REVERT: D 274 LYS cc_start: 0.8589 (ttpt) cc_final: 0.7928 (tppt) REVERT: D 426 GLU cc_start: 0.8547 (tp30) cc_final: 0.8130 (tp30) REVERT: D 440 ASN cc_start: 0.7876 (m-40) cc_final: 0.7539 (m110) REVERT: D 676 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: D 763 TYR cc_start: 0.8718 (m-80) cc_final: 0.8496 (m-80) REVERT: D 852 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8331 (ptp90) outliers start: 144 outliers final: 81 residues processed: 700 average time/residue: 0.5210 time to fit residues: 438.8431 Evaluate side-chains 658 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 573 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 794 THR Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 412 HIS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 676 GLU Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 289 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 253 optimal weight: 0.0470 chunk 286 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 272 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 292 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 308 ASN A 550 HIS A 987 GLN B 297 GLN B 550 HIS ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 550 HIS C 666 GLN D 297 GLN D 550 HIS D 993 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131134 restraints weight = 36015.695| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.35 r_work: 0.3336 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29240 Z= 0.134 Angle : 0.641 14.097 39516 Z= 0.321 Chirality : 0.043 0.193 4400 Planarity : 0.004 0.045 4816 Dihedral : 9.116 88.786 4256 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.07 % Allowed : 25.59 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3336 helix: 0.55 (0.11), residues: 2296 sheet: -2.35 (0.36), residues: 176 loop : -2.26 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 998 TYR 0.049 0.002 TYR B 784 PHE 0.023 0.001 PHE A 989 TRP 0.019 0.001 TRP D 888 HIS 0.005 0.001 HIS B 176 Details of bonding type rmsd covalent geometry : bond 0.00324 (29236) covalent geometry : angle 0.64090 (39516) hydrogen bonds : bond 0.03190 ( 1448) hydrogen bonds : angle 3.90314 ( 4320) Misc. bond : bond 0.00305 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 660 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8603 (tp40) cc_final: 0.8362 (tp40) REVERT: A 274 LYS cc_start: 0.8528 (ttpt) cc_final: 0.7884 (tppt) REVERT: A 374 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 426 GLU cc_start: 0.8523 (tp30) cc_final: 0.8109 (tp30) REVERT: A 439 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 440 ASN cc_start: 0.7848 (m-40) cc_final: 0.7411 (m110) REVERT: A 498 LYS cc_start: 0.8745 (tttm) cc_final: 0.8469 (tttm) REVERT: A 565 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8708 (tttp) REVERT: A 773 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: A 779 MET cc_start: 0.7372 (ppp) cc_final: 0.6907 (pmm) REVERT: A 788 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6802 (pt) REVERT: A 879 LEU cc_start: 0.7378 (mm) cc_final: 0.6771 (pp) REVERT: A 949 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7878 (tt) REVERT: A 971 TYR cc_start: 0.8606 (p90) cc_final: 0.8267 (p90) REVERT: A 984 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7332 (t60) REVERT: B 274 LYS cc_start: 0.8615 (ttpt) cc_final: 0.7873 (tppt) REVERT: B 371 TRP cc_start: 0.7306 (m100) cc_final: 0.7103 (m-10) REVERT: B 426 GLU cc_start: 0.8508 (tp30) cc_final: 0.8093 (tp30) REVERT: B 440 ASN cc_start: 0.7885 (m-40) cc_final: 0.7508 (m110) REVERT: B 676 GLU cc_start: 0.8414 (tp30) cc_final: 0.7991 (mp0) REVERT: B 773 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 852 ARG cc_start: 0.8279 (ttm170) cc_final: 0.7947 (ptp90) REVERT: B 879 LEU cc_start: 0.7513 (mm) cc_final: 0.6885 (pp) REVERT: B 949 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8176 (tt) REVERT: B 955 LEU cc_start: 0.9185 (mp) cc_final: 0.8973 (tp) REVERT: C 211 ILE cc_start: 0.8141 (pt) cc_final: 0.7857 (pp) REVERT: C 274 LYS cc_start: 0.8537 (ttpt) cc_final: 0.7848 (tppt) REVERT: C 374 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: C 426 GLU cc_start: 0.8492 (tp30) cc_final: 0.8112 (tp30) REVERT: C 440 ASN cc_start: 0.7852 (m-40) cc_final: 0.7478 (m110) REVERT: C 473 LEU cc_start: 0.8574 (tp) cc_final: 0.8349 (tt) REVERT: C 565 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8715 (tttp) REVERT: C 676 GLU cc_start: 0.8450 (tp30) cc_final: 0.8020 (mp0) REVERT: C 784 TYR cc_start: 0.6684 (t80) cc_final: 0.6390 (t80) REVERT: C 879 LEU cc_start: 0.7521 (mm) cc_final: 0.6902 (pp) REVERT: C 949 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8012 (tt) REVERT: C 1068 MET cc_start: 0.5676 (tpt) cc_final: 0.5363 (tpt) REVERT: D 211 ILE cc_start: 0.8159 (pt) cc_final: 0.7889 (pp) REVERT: D 274 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7877 (tppt) REVERT: D 426 GLU cc_start: 0.8510 (tp30) cc_final: 0.8088 (tp30) REVERT: D 440 ASN cc_start: 0.7874 (m-40) cc_final: 0.7521 (m110) REVERT: D 879 LEU cc_start: 0.7515 (mm) cc_final: 0.6899 (pp) REVERT: D 949 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7995 (tt) REVERT: D 984 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.7289 (t60) REVERT: D 1005 PHE cc_start: 0.7882 (m-10) cc_final: 0.7652 (m-80) outliers start: 125 outliers final: 73 residues processed: 734 average time/residue: 0.5368 time to fit residues: 472.5601 Evaluate side-chains 675 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 591 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 848 ILE Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 428 ASN Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 949 LEU Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 184 optimal weight: 0.8980 chunk 321 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 214 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN B 297 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN C 297 GLN D 190 ASN D 297 GLN D 308 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129365 restraints weight = 36224.304| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.36 r_work: 0.3332 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29240 Z= 0.161 Angle : 0.672 11.202 39516 Z= 0.339 Chirality : 0.044 0.196 4400 Planarity : 0.004 0.051 4816 Dihedral : 8.944 87.426 4256 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.13 % Allowed : 26.76 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3336 helix: 0.58 (0.11), residues: 2312 sheet: -2.44 (0.36), residues: 184 loop : -2.46 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 998 TYR 0.030 0.002 TYR B 763 PHE 0.023 0.001 PHE A 989 TRP 0.020 0.001 TRP D 888 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00395 (29236) covalent geometry : angle 0.67163 (39516) hydrogen bonds : bond 0.03328 ( 1448) hydrogen bonds : angle 3.92763 ( 4320) Misc. bond : bond 0.00315 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 623 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8702 (tp40) cc_final: 0.8419 (tp40) REVERT: A 274 LYS cc_start: 0.8502 (ttpt) cc_final: 0.7766 (mmmt) REVERT: A 374 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: A 426 GLU cc_start: 0.8568 (tp30) cc_final: 0.8145 (tp30) REVERT: A 439 THR cc_start: 0.7898 (OUTLIER) cc_final: 0.7395 (p) REVERT: A 440 ASN cc_start: 0.7843 (m-40) cc_final: 0.7415 (m110) REVERT: A 498 LYS cc_start: 0.8740 (tttm) cc_final: 0.8486 (tttm) REVERT: A 565 LYS cc_start: 0.9085 (ttmm) cc_final: 0.8699 (tttp) REVERT: A 773 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 784 TYR cc_start: 0.6144 (t80) cc_final: 0.5702 (t80) REVERT: A 949 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7993 (tt) REVERT: A 971 TYR cc_start: 0.8542 (p90) cc_final: 0.8273 (p90) REVERT: A 994 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 1068 MET cc_start: 0.5725 (tpt) cc_final: 0.5310 (tpt) REVERT: B 274 LYS cc_start: 0.8548 (ttpt) cc_final: 0.7848 (tppt) REVERT: B 371 TRP cc_start: 0.7315 (m100) cc_final: 0.7106 (m-10) REVERT: B 426 GLU cc_start: 0.8535 (tp30) cc_final: 0.8149 (tp30) REVERT: B 439 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7453 (p) REVERT: B 440 ASN cc_start: 0.7879 (m-40) cc_final: 0.7488 (m110) REVERT: B 565 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8716 (tttp) REVERT: B 676 GLU cc_start: 0.8414 (tp30) cc_final: 0.7971 (mp0) REVERT: B 773 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 784 TYR cc_start: 0.7570 (t80) cc_final: 0.7351 (t80) REVERT: B 852 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8051 (ptp90) REVERT: B 853 MET cc_start: 0.8772 (ttp) cc_final: 0.8520 (ttp) REVERT: B 955 LEU cc_start: 0.9210 (mp) cc_final: 0.8924 (tp) REVERT: B 1068 MET cc_start: 0.5734 (tpt) cc_final: 0.5509 (tpt) REVERT: C 211 ILE cc_start: 0.8119 (pt) cc_final: 0.7799 (pp) REVERT: C 274 LYS cc_start: 0.8591 (ttpt) cc_final: 0.7740 (tppt) REVERT: C 278 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8090 (mp0) REVERT: C 374 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: C 426 GLU cc_start: 0.8517 (tp30) cc_final: 0.8129 (tp30) REVERT: C 439 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7399 (p) REVERT: C 440 ASN cc_start: 0.7831 (m-40) cc_final: 0.7425 (m110) REVERT: C 565 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8667 (tttp) REVERT: C 676 GLU cc_start: 0.8434 (tp30) cc_final: 0.7998 (mp0) REVERT: C 1001 ILE cc_start: 0.8801 (mt) cc_final: 0.8588 (pp) REVERT: C 1068 MET cc_start: 0.5532 (tpt) cc_final: 0.5300 (tpt) REVERT: D 211 ILE cc_start: 0.8124 (pt) cc_final: 0.7835 (pp) REVERT: D 274 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7896 (tppt) REVERT: D 426 GLU cc_start: 0.8532 (tp30) cc_final: 0.8140 (tp30) REVERT: D 439 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7398 (p) REVERT: D 440 ASN cc_start: 0.7815 (m-40) cc_final: 0.7430 (m110) REVERT: D 852 ARG cc_start: 0.8485 (ptp90) cc_final: 0.8223 (ptp90) REVERT: D 1005 PHE cc_start: 0.7967 (m-10) cc_final: 0.7732 (m-80) REVERT: D 1068 MET cc_start: 0.5523 (tpt) cc_final: 0.5308 (tpt) outliers start: 127 outliers final: 77 residues processed: 694 average time/residue: 0.5414 time to fit residues: 450.7975 Evaluate side-chains 662 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 578 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 695 LEU Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 794 THR Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 111 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 294 optimal weight: 0.0010 chunk 249 optimal weight: 2.9990 chunk 275 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 254 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 657 GLN A 835 HIS B 297 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 851 GLN C 993 GLN D 297 GLN D 851 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.171555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129127 restraints weight = 36187.636| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.36 r_work: 0.3307 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29240 Z= 0.175 Angle : 0.700 16.632 39516 Z= 0.351 Chirality : 0.044 0.194 4400 Planarity : 0.004 0.043 4816 Dihedral : 8.873 88.577 4256 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.87 % Allowed : 27.18 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3336 helix: 0.56 (0.11), residues: 2316 sheet: -2.42 (0.36), residues: 184 loop : -2.49 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 998 TYR 0.031 0.002 TYR B 763 PHE 0.024 0.001 PHE A 989 TRP 0.021 0.002 TRP A 888 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00426 (29236) covalent geometry : angle 0.70041 (39516) hydrogen bonds : bond 0.03378 ( 1448) hydrogen bonds : angle 3.96973 ( 4320) Misc. bond : bond 0.00325 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 601 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLN cc_start: 0.8710 (tp40) cc_final: 0.8461 (tp40) REVERT: A 203 ILE cc_start: 0.9131 (mt) cc_final: 0.8873 (mm) REVERT: A 233 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7180 (mtm) REVERT: A 274 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7908 (mmmt) REVERT: A 374 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: A 426 GLU cc_start: 0.8595 (tp30) cc_final: 0.8168 (tp30) REVERT: A 439 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7435 (p) REVERT: A 440 ASN cc_start: 0.7842 (m-40) cc_final: 0.7431 (m110) REVERT: A 498 LYS cc_start: 0.8740 (tttm) cc_final: 0.8398 (tttm) REVERT: A 773 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 779 MET cc_start: 0.7389 (ppp) cc_final: 0.6471 (pmm) REVERT: A 793 ASP cc_start: 0.8231 (m-30) cc_final: 0.8023 (m-30) REVERT: A 853 MET cc_start: 0.9170 (mtt) cc_final: 0.8884 (mtt) REVERT: A 949 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8015 (tt) REVERT: A 971 TYR cc_start: 0.8588 (p90) cc_final: 0.8316 (p90) REVERT: A 1068 MET cc_start: 0.5859 (tpt) cc_final: 0.5503 (tpt) REVERT: B 274 LYS cc_start: 0.8482 (ttpt) cc_final: 0.7868 (tppt) REVERT: B 371 TRP cc_start: 0.7307 (m100) cc_final: 0.7105 (m-10) REVERT: B 426 GLU cc_start: 0.8571 (tp30) cc_final: 0.8161 (tp30) REVERT: B 439 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7377 (p) REVERT: B 440 ASN cc_start: 0.7861 (m-40) cc_final: 0.7439 (m110) REVERT: B 565 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8674 (tttp) REVERT: B 676 GLU cc_start: 0.8420 (tp30) cc_final: 0.7981 (mp0) REVERT: B 773 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: B 784 TYR cc_start: 0.7439 (t80) cc_final: 0.7228 (t80) REVERT: B 955 LEU cc_start: 0.9177 (mp) cc_final: 0.8915 (tp) REVERT: B 1068 MET cc_start: 0.5802 (tpt) cc_final: 0.5565 (tpt) REVERT: C 211 ILE cc_start: 0.8034 (pt) cc_final: 0.7761 (pp) REVERT: C 274 LYS cc_start: 0.8554 (ttpt) cc_final: 0.7803 (tppt) REVERT: C 278 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 374 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: C 426 GLU cc_start: 0.8545 (tp30) cc_final: 0.8150 (tp30) REVERT: C 439 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7334 (p) REVERT: C 440 ASN cc_start: 0.7838 (m-40) cc_final: 0.7444 (m110) REVERT: C 1068 MET cc_start: 0.5690 (tpt) cc_final: 0.5383 (tpt) REVERT: D 211 ILE cc_start: 0.8040 (pt) cc_final: 0.7766 (pp) REVERT: D 274 LYS cc_start: 0.8520 (ttpt) cc_final: 0.7798 (mmmt) REVERT: D 426 GLU cc_start: 0.8570 (tp30) cc_final: 0.8157 (tp30) REVERT: D 439 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7325 (p) REVERT: D 440 ASN cc_start: 0.7808 (m-40) cc_final: 0.7421 (m110) REVERT: D 565 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8745 (tttp) REVERT: D 1068 MET cc_start: 0.5576 (tpt) cc_final: 0.5307 (tpt) outliers start: 119 outliers final: 74 residues processed: 670 average time/residue: 0.5337 time to fit residues: 428.0836 Evaluate side-chains 655 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 572 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 MET Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 230 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 993 GLN D 297 GLN D 993 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129512 restraints weight = 35949.966| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.33 r_work: 0.3306 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29240 Z= 0.175 Angle : 0.721 16.055 39516 Z= 0.358 Chirality : 0.045 0.195 4400 Planarity : 0.004 0.041 4816 Dihedral : 8.752 89.777 4256 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.45 % Allowed : 27.93 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.15), residues: 3336 helix: 0.53 (0.11), residues: 2328 sheet: -2.22 (0.37), residues: 176 loop : -2.43 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 998 TYR 0.036 0.002 TYR B 763 PHE 0.026 0.002 PHE A 989 TRP 0.021 0.002 TRP D 888 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00427 (29236) covalent geometry : angle 0.72141 (39516) hydrogen bonds : bond 0.03388 ( 1448) hydrogen bonds : angle 3.96832 ( 4320) Misc. bond : bond 0.00319 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 594 time to evaluate : 0.932 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: A 164 GLN cc_start: 0.8718 (tp40) cc_final: 0.8483 (tp40) REVERT: A 203 ILE cc_start: 0.9136 (mt) cc_final: 0.8866 (mm) REVERT: A 233 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7199 (mtm) REVERT: A 274 LYS cc_start: 0.8698 (ttpt) cc_final: 0.7838 (mmmt) REVERT: A 278 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8346 (mp0) REVERT: A 374 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: A 389 GLU cc_start: 0.7734 (mp0) cc_final: 0.7427 (pm20) REVERT: A 426 GLU cc_start: 0.8600 (tp30) cc_final: 0.8172 (tp30) REVERT: A 440 ASN cc_start: 0.7787 (m-40) cc_final: 0.7364 (m110) REVERT: A 498 LYS cc_start: 0.8736 (tttm) cc_final: 0.8387 (tttm) REVERT: A 773 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: A 779 MET cc_start: 0.7224 (ppp) cc_final: 0.6538 (pmm) REVERT: A 793 ASP cc_start: 0.8324 (m-30) cc_final: 0.8111 (m-30) REVERT: A 853 MET cc_start: 0.9147 (mtt) cc_final: 0.8870 (mtt) REVERT: A 949 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8021 (tt) REVERT: A 971 TYR cc_start: 0.8589 (p90) cc_final: 0.8323 (p90) REVERT: A 994 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 1068 MET cc_start: 0.5788 (tpt) cc_final: 0.5462 (tpt) REVERT: B 389 GLU cc_start: 0.7837 (mp0) cc_final: 0.7543 (pm20) REVERT: B 426 GLU cc_start: 0.8545 (tp30) cc_final: 0.8143 (tp30) REVERT: B 439 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7512 (p) REVERT: B 440 ASN cc_start: 0.7832 (m-40) cc_final: 0.7407 (m110) REVERT: B 676 GLU cc_start: 0.8427 (tp30) cc_final: 0.7994 (mp0) REVERT: B 773 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: B 853 MET cc_start: 0.8876 (ttp) cc_final: 0.8612 (ttp) REVERT: B 955 LEU cc_start: 0.9189 (mp) cc_final: 0.8943 (tp) REVERT: C 211 ILE cc_start: 0.8010 (pt) cc_final: 0.7731 (pp) REVERT: C 374 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: C 426 GLU cc_start: 0.8533 (tp30) cc_final: 0.8141 (tp30) REVERT: C 440 ASN cc_start: 0.7808 (m-40) cc_final: 0.7425 (m110) REVERT: C 852 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8262 (ptp90) REVERT: C 893 VAL cc_start: 0.8608 (p) cc_final: 0.8401 (t) REVERT: C 1068 MET cc_start: 0.5489 (tpt) cc_final: 0.5200 (tpt) REVERT: D 211 ILE cc_start: 0.8043 (pt) cc_final: 0.7761 (pp) REVERT: D 274 LYS cc_start: 0.8509 (ttpt) cc_final: 0.7794 (mmmt) REVERT: D 426 GLU cc_start: 0.8556 (tp30) cc_final: 0.8154 (tp30) REVERT: D 440 ASN cc_start: 0.7795 (m-40) cc_final: 0.7415 (m110) REVERT: D 565 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8615 (tttp) REVERT: D 753 LYS cc_start: 0.7554 (tppp) cc_final: 0.6994 (mmmt) REVERT: D 1068 MET cc_start: 0.5888 (tpt) cc_final: 0.5543 (tpt) outliers start: 106 outliers final: 76 residues processed: 657 average time/residue: 0.5382 time to fit residues: 423.8696 Evaluate side-chains 650 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 567 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 809 HIS Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 984 TRP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 809 HIS Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 946 THR Chi-restraints excluded: chain B residue 984 TRP Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 809 HIS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 984 TRP Chi-restraints excluded: chain C residue 1007 ILE Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 317 CYS Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 809 HIS Chi-restraints excluded: chain D residue 848 ILE Chi-restraints excluded: chain D residue 878 ILE Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 946 THR Chi-restraints excluded: chain D residue 984 TRP Chi-restraints excluded: chain D residue 1007 ILE Chi-restraints excluded: chain D residue 1048 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 166 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 987 GLN C 297 GLN C 993 GLN D 297 GLN D 993 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130716 restraints weight = 36225.468| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.36 r_work: 0.3324 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 29240 Z= 0.148 Angle : 0.715 15.178 39516 Z= 0.351 Chirality : 0.044 0.198 4400 Planarity : 0.004 0.042 4816 Dihedral : 8.518 89.829 4256 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.16 % Allowed : 28.55 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3336 helix: 0.62 (0.11), residues: 2336 sheet: -2.16 (0.38), residues: 176 loop : -2.42 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 998 TYR 0.025 0.002 TYR C 286 PHE 0.036 0.001 PHE A 989 TRP 0.022 0.001 TRP A 888 HIS 0.007 0.001 HIS A 176 Details of bonding type rmsd covalent geometry : bond 0.00362 (29236) covalent geometry : angle 0.71518 (39516) hydrogen bonds : bond 0.03286 ( 1448) hydrogen bonds : angle 3.91156 ( 4320) Misc. bond : bond 0.00270 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9484.34 seconds wall clock time: 162 minutes 8.78 seconds (9728.78 seconds total)