Starting phenix.real_space_refine on Mon Dec 22 07:27:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9k_8786/12_2025/5w9k_8786.cif" } resolution = 4.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20849 2.51 5 N 5462 2.21 5 O 6382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 233 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32873 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3531 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 436} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3538 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3527 Classifications: {'peptide': 460} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5645 Classifications: {'peptide': 724} Link IDs: {'CIS': 3, 'PTRANS': 35, 'TRANS': 685} Chain: "K" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5645 Classifications: {'peptide': 724} Link IDs: {'CIS': 5, 'PTRANS': 35, 'TRANS': 683} Chain: "L" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5638 Classifications: {'peptide': 723} Link IDs: {'CIS': 3, 'PTRANS': 35, 'TRANS': 684} Time building chain proxies: 7.80, per 1000 atoms: 0.24 Number of scatterers: 32873 At special positions: 0 Unit cell: (166.26, 154.02, 223.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6382 8.00 N 5462 7.00 C 20849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=1.99 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.08 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.19 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.07 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.17 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.11 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.07 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.87 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.09 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.07 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.65 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.04 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.08 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=1.78 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.04 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=1.63 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=1.80 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.05 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.05 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.03 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.04 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.83 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.01 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.13 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.03 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.09 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=1.77 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=1.98 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.07 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.14 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.04 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.43 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=2.33 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=1.90 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=1.68 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=1.79 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7878 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 77 sheets defined 23.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.154A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.893A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.640A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.797A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.764A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 822 removed outlier: 3.790A pdb=" N ARG D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.851A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 4.756A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1040 removed outlier: 3.525A pdb=" N ASN D1029 " --> pdb=" O ALA D1025 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 4.051A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.669A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.513A pdb=" N THR F 83 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 822 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.847A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 912 removed outlier: 3.502A pdb=" N ASP G 910 " --> pdb=" O GLN G 907 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.762A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.716A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.734A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G1066 " --> pdb=" O GLU G1062 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.517A pdb=" N ASP J 41 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.573A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 removed outlier: 3.735A pdb=" N PHE J 399 " --> pdb=" O VAL J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 415 Processing helix chain 'J' and resid 416 through 418 No H-bonds generated for 'chain 'J' and resid 416 through 418' Processing helix chain 'J' and resid 429 through 436 removed outlier: 4.114A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.872A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 675 through 678 removed outlier: 3.645A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 3.518A pdb=" N LYS J 698 " --> pdb=" O ARG J 694 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 4.069A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 303 through 307 removed outlier: 3.975A pdb=" N ARG K 307 " --> pdb=" O GLN K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.572A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.577A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 449 through 456 removed outlier: 5.232A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 675 through 682 removed outlier: 3.619A pdb=" N ALA K 678 " --> pdb=" O GLY K 675 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS K 679 " --> pdb=" O SER K 676 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU K 680 " --> pdb=" O VAL K 677 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 702 removed outlier: 3.590A pdb=" N LYS K 698 " --> pdb=" O ARG K 694 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.529A pdb=" N ASP L 41 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 133 through 137 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 303 through 307 removed outlier: 3.751A pdb=" N ARG L 307 " --> pdb=" O GLN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 390 removed outlier: 3.546A pdb=" N SER L 390 " --> pdb=" O PRO L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 399 removed outlier: 3.763A pdb=" N PHE L 399 " --> pdb=" O VAL L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 415 Processing helix chain 'L' and resid 416 through 418 No H-bonds generated for 'chain 'L' and resid 416 through 418' Processing helix chain 'L' and resid 429 through 436 removed outlier: 4.026A pdb=" N ALA L 434 " --> pdb=" O PRO L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 456 removed outlier: 5.001A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 675 through 678 removed outlier: 3.649A pdb=" N ALA L 678 " --> pdb=" O GLY L 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 675 through 678' Processing helix chain 'L' and resid 694 through 702 removed outlier: 3.572A pdb=" N LYS L 698 " --> pdb=" O ARG L 694 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.373A pdb=" N LEU A 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU J 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.810A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.913A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.278A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.462A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.481A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.912A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 719 through 724 removed outlier: 7.360A pdb=" N LEU D 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU K 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY K 732 " --> pdb=" O LEU K 735 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA K 737 " --> pdb=" O PRO K 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.720A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.824A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.343A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.782A pdb=" N ALA E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.356A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.356A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.850A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 719 through 724 removed outlier: 7.327A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.862A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1204 removed outlier: 6.431A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.522A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.576A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.891A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 63 through 64 removed outlier: 6.301A pdb=" N THR J 63 " --> pdb=" O TYR L 632 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 68 through 72 removed outlier: 3.552A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AE2, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.490A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.527A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.443A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 185 " --> pdb=" O THR J 168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.443A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 185 " --> pdb=" O THR J 168 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.376A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE9, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.131A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.596A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY J 615 " --> pdb=" O VAL J 604 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.574A pdb=" N THR J 477 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.444A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.038A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AF6, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.620A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AF8, first strand: chain 'K' and resid 75 through 76 removed outlier: 6.535A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.626A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AG2, first strand: chain 'K' and resid 110 through 111 removed outlier: 4.425A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU K 180 " --> pdb=" O THR K 242 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR K 242 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA K 182 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET K 240 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR K 184 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE K 186 " --> pdb=" O ASN K 236 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASN K 236 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU K 188 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU K 234 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 126 through 127 removed outlier: 4.422A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 309 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG5, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.185A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG7, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.209A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 573 " --> pdb=" O CYS K 478 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU K 479 " --> pdb=" O PHE K 423 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE K 423 " --> pdb=" O LEU K 479 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU K 481 " --> pdb=" O ASN K 421 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.500A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 617 through 618 removed outlier: 5.634A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AH3, first strand: chain 'L' and resid 68 through 72 removed outlier: 3.602A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 75 through 76 Processing sheet with id=AH5, first strand: chain 'L' and resid 75 through 76 removed outlier: 6.254A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 88 through 89 removed outlier: 3.974A pdb=" N SER L 88 " --> pdb=" O HIS L 298 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH8, first strand: chain 'L' and resid 110 through 111 removed outlier: 4.594A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU L 180 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR L 241 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA L 182 " --> pdb=" O PHE L 239 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE L 239 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR L 184 " --> pdb=" O CYS L 237 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS L 237 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 126 through 127 removed outlier: 4.623A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA L 309 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.334A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 374 through 376 removed outlier: 3.844A pdb=" N GLY L 615 " --> pdb=" O VAL L 604 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 400 through 404 removed outlier: 7.257A pdb=" N LEU L 479 " --> pdb=" O PHE L 423 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE L 423 " --> pdb=" O LEU L 479 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU L 481 " --> pdb=" O ASN L 421 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.401A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3276 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: 9.37 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6859 1.32 - 1.46: 10752 1.46 - 1.59: 15786 1.59 - 1.72: 2 1.72 - 1.85: 246 Bond restraints: 33645 Sorted by residual: bond pdb=" N ILE L 186 " pdb=" CA ILE L 186 " ideal model delta sigma weight residual 1.459 1.557 -0.098 1.19e-02 7.06e+03 6.74e+01 bond pdb=" CA CYS J 425 " pdb=" C CYS J 425 " ideal model delta sigma weight residual 1.522 1.426 0.096 1.24e-02 6.50e+03 5.96e+01 bond pdb=" CA CYS K 185 " pdb=" C CYS K 185 " ideal model delta sigma weight residual 1.522 1.616 -0.094 1.24e-02 6.50e+03 5.78e+01 bond pdb=" C CYS K 437 " pdb=" N TYR K 438 " ideal model delta sigma weight residual 1.331 1.429 -0.098 1.33e-02 5.65e+03 5.43e+01 bond pdb=" C ASN L 236 " pdb=" N CYS L 237 " ideal model delta sigma weight residual 1.330 1.413 -0.083 1.38e-02 5.25e+03 3.60e+01 ... (remaining 33640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 43134 3.54 - 7.08: 2370 7.08 - 10.61: 225 10.61 - 14.15: 15 14.15 - 17.69: 2 Bond angle restraints: 45746 Sorted by residual: angle pdb=" N CYS L 736 " pdb=" CA CYS L 736 " pdb=" C CYS L 736 " ideal model delta sigma weight residual 108.96 91.27 17.69 1.49e+00 4.50e-01 1.41e+02 angle pdb=" O CYS L 185 " pdb=" C CYS L 185 " pdb=" N ILE L 186 " ideal model delta sigma weight residual 123.10 110.99 12.11 1.15e+00 7.56e-01 1.11e+02 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.97 -7.31 7.20e-01 1.93e+00 1.03e+02 angle pdb=" C VAL I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta sigma weight residual 119.92 130.56 -10.64 1.07e+00 8.73e-01 9.88e+01 angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.92 130.50 -10.58 1.07e+00 8.73e-01 9.78e+01 ... (remaining 45741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 19293 17.55 - 35.10: 519 35.10 - 52.64: 165 52.64 - 70.19: 86 70.19 - 87.74: 17 Dihedral angle restraints: 20080 sinusoidal: 7727 harmonic: 12353 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.99 -74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.24 -72.24 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 20077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4091 0.104 - 0.208: 917 0.208 - 0.312: 60 0.312 - 0.416: 4 0.416 - 0.520: 3 Chirality restraints: 5075 Sorted by residual: chirality pdb=" CA CYS J 736 " pdb=" N CYS J 736 " pdb=" C CYS J 736 " pdb=" CB CYS J 736 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CA CYS J 383 " pdb=" N CYS J 383 " pdb=" C CYS J 383 " pdb=" CB CYS J 383 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA CYS L 736 " pdb=" N CYS L 736 " pdb=" C CYS L 736 " pdb=" CB CYS L 736 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 5072 not shown) Planarity restraints: 5942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.084 2.00e-02 2.50e+03 4.14e-02 4.28e+01 pdb=" CG TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.079 2.00e-02 2.50e+03 3.92e-02 3.85e+01 pdb=" CG TRP H 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 642 " -0.076 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" CG TYR K 642 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR K 642 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR K 642 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR K 642 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR K 642 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR K 642 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR K 642 " -0.062 2.00e-02 2.50e+03 ... (remaining 5939 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 20 2.05 - 2.77: 6298 2.77 - 3.48: 44263 3.48 - 4.19: 79715 4.19 - 4.90: 134222 Nonbonded interactions: 264518 Sorted by model distance: nonbonded pdb=" OH TYR G 905 " pdb=" CA PRO G 936 " model vdw 1.342 3.470 nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.458 3.470 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.523 3.760 nonbonded pdb=" OH TYR A 905 " pdb=" CB PRO A 936 " model vdw 1.544 3.440 nonbonded pdb=" OH TYR G 905 " pdb=" CB PRO G 936 " model vdw 1.557 3.440 ... (remaining 264513 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 756 through 1223) selection = (chain 'D' and resid 756 through 1223) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = (chain 'J' and resid 18 through 740) selection = (chain 'K' and resid 18 through 740) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.030 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.650 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.016 0.837 33702 Z= 0.961 Angle : 1.782 28.724 45860 Z= 1.204 Chirality : 0.083 0.520 5075 Planarity : 0.012 0.133 5942 Dihedral : 10.395 87.738 12031 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.65 % Favored : 95.73 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 1.72 (0.13), residues: 4214 helix: -0.35 (0.16), residues: 657 sheet: 0.85 (0.16), residues: 940 loop : 1.95 (0.13), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 94 TYR 0.076 0.007 TYR K 642 PHE 0.062 0.005 PHE F 98 TRP 0.084 0.009 TRP B 47 HIS 0.007 0.002 HIS K 681 Details of bonding type rmsd covalent geometry : bond 0.01344 (33645) covalent geometry : angle 1.74057 (45746) SS BOND : bond 0.21366 ( 57) SS BOND : angle 7.86050 ( 114) hydrogen bonds : bond 0.19891 ( 1257) hydrogen bonds : angle 8.10691 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 848 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 794 TYR cc_start: 0.9172 (t80) cc_final: 0.8762 (t80) REVERT: A 805 ASP cc_start: 0.8360 (t0) cc_final: 0.7487 (m-30) REVERT: A 843 ASP cc_start: 0.8351 (m-30) cc_final: 0.8087 (m-30) REVERT: A 943 MET cc_start: 0.9244 (mtp) cc_final: 0.8656 (ttp) REVERT: A 978 TYR cc_start: 0.8576 (t80) cc_final: 0.8307 (t80) REVERT: A 980 LEU cc_start: 0.9556 (mt) cc_final: 0.9323 (mm) REVERT: A 1138 HIS cc_start: 0.9138 (m-70) cc_final: 0.8705 (m-70) REVERT: B 4 LEU cc_start: 0.7446 (mt) cc_final: 0.7219 (mt) REVERT: B 5 GLN cc_start: 0.8014 (tp40) cc_final: 0.7443 (mp10) REVERT: B 18 VAL cc_start: 0.6037 (p) cc_final: 0.5745 (t) REVERT: B 61 GLN cc_start: 0.9232 (mt0) cc_final: 0.8765 (pp30) REVERT: B 69 MET cc_start: 0.6274 (mtt) cc_final: 0.3993 (mtt) REVERT: B 81 GLU cc_start: 0.8374 (tt0) cc_final: 0.7905 (tm-30) REVERT: B 82 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7445 (mtm180) REVERT: C 35 TRP cc_start: 0.6874 (m100) cc_final: 0.6470 (m100) REVERT: C 42 GLN cc_start: 0.8256 (pt0) cc_final: 0.7902 (mp10) REVERT: C 44 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.7949 (Cg_exo) REVERT: C 62 PHE cc_start: 0.8080 (m-80) cc_final: 0.7799 (m-80) REVERT: C 70 ASP cc_start: 0.9008 (t70) cc_final: 0.8690 (p0) REVERT: C 73 LEU cc_start: 0.7821 (tp) cc_final: 0.7217 (tp) REVERT: C 92 LYS cc_start: 0.8824 (tmtt) cc_final: 0.8590 (tttp) REVERT: D 821 LEU cc_start: 0.8926 (tp) cc_final: 0.8531 (tp) REVERT: D 843 ASP cc_start: 0.8607 (m-30) cc_final: 0.8296 (t0) REVERT: D 938 LEU cc_start: 0.8955 (tp) cc_final: 0.8573 (tp) REVERT: D 1033 LEU cc_start: 0.9565 (mt) cc_final: 0.9201 (tp) REVERT: D 1141 TYR cc_start: 0.7818 (t80) cc_final: 0.7477 (t80) REVERT: E 2 VAL cc_start: 0.6649 (t) cc_final: 0.5518 (t) REVERT: E 69 MET cc_start: 0.7600 (mtt) cc_final: 0.6560 (mtt) REVERT: E 85 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7701 (pt0) REVERT: E 103 TRP cc_start: 0.5176 (m-90) cc_final: 0.3815 (m100) REVERT: F 2 ILE cc_start: 0.8826 (mp) cc_final: 0.8069 (mm) REVERT: F 11 LEU cc_start: 0.7633 (tp) cc_final: 0.7336 (pp) REVERT: F 27 GLU cc_start: 0.8455 (tt0) cc_final: 0.8162 (tm-30) REVERT: F 42 GLN cc_start: 0.7574 (pt0) cc_final: 0.7041 (mp10) REVERT: F 80 GLU cc_start: 0.6760 (pm20) cc_final: 0.6321 (tm-30) REVERT: F 89 GLN cc_start: 0.7649 (tt0) cc_final: 0.7050 (tm-30) REVERT: F 91 SER cc_start: 0.8059 (m) cc_final: 0.7835 (p) REVERT: F 98 PHE cc_start: 0.7011 (p90) cc_final: 0.6727 (p90) REVERT: G 816 LYS cc_start: 0.7779 (tptt) cc_final: 0.7572 (tttt) REVERT: G 906 MET cc_start: 0.5704 (mmp) cc_final: 0.4964 (mmm) REVERT: G 932 TYR cc_start: 0.6957 (m-10) cc_final: 0.6449 (m-10) REVERT: G 938 LEU cc_start: 0.9408 (tp) cc_final: 0.9037 (tp) REVERT: G 1027 ASN cc_start: 0.8657 (m-40) cc_final: 0.8282 (t0) REVERT: G 1104 ASN cc_start: 0.9343 (m-40) cc_final: 0.8843 (t0) REVERT: G 1191 PHE cc_start: 0.8309 (t80) cc_final: 0.7762 (t80) REVERT: H 18 VAL cc_start: 0.8764 (p) cc_final: 0.8466 (p) REVERT: H 23 LYS cc_start: 0.9222 (tttt) cc_final: 0.8683 (ptpp) REVERT: H 31 ASP cc_start: 0.8450 (m-30) cc_final: 0.7606 (t70) REVERT: H 35 HIS cc_start: 0.9049 (m-70) cc_final: 0.8421 (m170) REVERT: H 66 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7430 (mmt90) REVERT: I 33 MET cc_start: 0.7328 (tpp) cc_final: 0.6582 (tpp) REVERT: I 35 TRP cc_start: 0.6640 (m100) cc_final: 0.6278 (m100) REVERT: I 36 PHE cc_start: 0.9295 (m-80) cc_final: 0.8574 (m-80) REVERT: I 47 LEU cc_start: 0.7735 (mt) cc_final: 0.7490 (mm) REVERT: I 73 LEU cc_start: 0.8526 (tp) cc_final: 0.8171 (tp) REVERT: I 102 THR cc_start: 0.7141 (p) cc_final: 0.6257 (t) REVERT: I 104 LEU cc_start: 0.8392 (tp) cc_final: 0.7917 (tp) REVERT: J 71 TYR cc_start: 0.8184 (t80) cc_final: 0.7614 (t80) REVERT: J 86 VAL cc_start: 0.8063 (t) cc_final: 0.6629 (t) REVERT: J 116 PHE cc_start: 0.9289 (p90) cc_final: 0.8725 (p90) REVERT: J 204 PHE cc_start: 0.6833 (t80) cc_final: 0.6379 (t80) REVERT: J 278 MET cc_start: 0.8477 (mtp) cc_final: 0.7773 (tpp) REVERT: J 293 TYR cc_start: 0.7871 (t80) cc_final: 0.7447 (t80) REVERT: J 296 ILE cc_start: 0.8646 (mt) cc_final: 0.8100 (mt) REVERT: J 389 LEU cc_start: 0.8260 (mt) cc_final: 0.7886 (pp) REVERT: J 651 LEU cc_start: 0.9391 (tp) cc_final: 0.9111 (tp) REVERT: J 717 LEU cc_start: 0.8589 (mm) cc_final: 0.8332 (mt) REVERT: J 726 ASP cc_start: 0.7859 (t0) cc_final: 0.7283 (p0) REVERT: J 731 LEU cc_start: 0.9045 (mt) cc_final: 0.8665 (mp) REVERT: K 52 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8977 (mmmt) REVERT: K 120 ILE cc_start: 0.9472 (mt) cc_final: 0.9260 (tp) REVERT: K 126 SER cc_start: 0.8700 (t) cc_final: 0.8403 (p) REVERT: K 317 LYS cc_start: 0.9295 (mttt) cc_final: 0.8963 (mmmt) REVERT: K 318 LEU cc_start: 0.9183 (mt) cc_final: 0.8895 (mt) REVERT: K 323 PHE cc_start: 0.8990 (m-80) cc_final: 0.8695 (m-10) REVERT: K 337 ILE cc_start: 0.9183 (mt) cc_final: 0.8912 (mm) REVERT: K 452 MET cc_start: 0.5533 (mmm) cc_final: 0.5051 (ttt) REVERT: K 472 SER cc_start: 0.6980 (t) cc_final: 0.6748 (p) REVERT: K 618 GLN cc_start: 0.9023 (pt0) cc_final: 0.8699 (tm-30) REVERT: K 629 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7309 (mtp180) REVERT: L 36 GLN cc_start: 0.7526 (mm-40) cc_final: 0.6889 (mp10) REVERT: L 149 LEU cc_start: 0.8909 (mp) cc_final: 0.8675 (mt) REVERT: L 180 LEU cc_start: 0.8649 (tp) cc_final: 0.8448 (tp) REVERT: L 218 ASN cc_start: 0.8789 (t0) cc_final: 0.8122 (p0) REVERT: L 587 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7448 (mtpp) REVERT: L 605 GLU cc_start: 0.9033 (tt0) cc_final: 0.8764 (tp30) REVERT: L 637 ASN cc_start: 0.8339 (m-40) cc_final: 0.7895 (m110) REVERT: L 693 THR cc_start: 0.4019 (t) cc_final: 0.3470 (p) outliers start: 5 outliers final: 1 residues processed: 853 average time/residue: 0.2219 time to fit residues: 302.4911 Evaluate side-chains 425 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.0170 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 overall best weight: 3.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A1104 ASN A1129 ASN B 41 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS D 792 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27DASN F 42 GLN F 74 ASN ** G 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 974 GLN G 993 ASN G1027 ASN G1097 GLN G1129 ASN G1208 GLN H 41 HIS I 76 HIS I 90 GLN K 377 GLN L 261 GLN L 377 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.089478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069863 restraints weight = 192679.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.071276 restraints weight = 127872.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071258 restraints weight = 96553.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071771 restraints weight = 81761.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071946 restraints weight = 70974.278| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33702 Z= 0.188 Angle : 0.737 10.638 45860 Z= 0.409 Chirality : 0.046 0.333 5075 Planarity : 0.007 0.100 5942 Dihedral : 5.742 26.440 4616 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.30 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 1.23 (0.13), residues: 4214 helix: 0.93 (0.19), residues: 692 sheet: 0.48 (0.15), residues: 1022 loop : 1.14 (0.13), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 614 TYR 0.034 0.002 TYR G 905 PHE 0.041 0.002 PHE J 101 TRP 0.021 0.002 TRP H 36 HIS 0.007 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00401 (33645) covalent geometry : angle 0.73402 (45746) SS BOND : bond 0.00468 ( 57) SS BOND : angle 1.57070 ( 114) hydrogen bonds : bond 0.06267 ( 1257) hydrogen bonds : angle 6.51655 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8938 (t80) cc_final: 0.8511 (t80) REVERT: A 805 ASP cc_start: 0.8528 (t0) cc_final: 0.7457 (m-30) REVERT: A 932 TYR cc_start: 0.5545 (m-10) cc_final: 0.5108 (m-10) REVERT: A 943 MET cc_start: 0.8901 (mtp) cc_final: 0.8272 (ttp) REVERT: A 980 LEU cc_start: 0.9507 (mt) cc_final: 0.9274 (mm) REVERT: A 1058 LEU cc_start: 0.8065 (mt) cc_final: 0.7059 (mt) REVERT: A 1177 ASN cc_start: 0.8533 (t0) cc_final: 0.8176 (t0) REVERT: B 5 GLN cc_start: 0.8274 (tp40) cc_final: 0.7646 (mp10) REVERT: B 6 GLN cc_start: 0.6264 (tp-100) cc_final: 0.5882 (tp40) REVERT: B 39 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 48 ILE cc_start: 0.8402 (mm) cc_final: 0.8147 (mm) REVERT: B 72 ASP cc_start: 0.8520 (t0) cc_final: 0.8244 (t0) REVERT: B 76 SER cc_start: 0.9435 (m) cc_final: 0.8838 (p) REVERT: B 81 GLU cc_start: 0.8461 (tt0) cc_final: 0.7749 (tp30) REVERT: B 82 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7380 (mtm180) REVERT: B 108 SER cc_start: 0.8637 (p) cc_final: 0.8431 (t) REVERT: C 18 ARG cc_start: 0.6933 (ttt-90) cc_final: 0.6661 (ttt-90) REVERT: C 42 GLN cc_start: 0.7847 (pt0) cc_final: 0.7337 (mp10) REVERT: C 44 PRO cc_start: 0.8352 (Cg_endo) cc_final: 0.8075 (Cg_exo) REVERT: C 70 ASP cc_start: 0.8801 (t70) cc_final: 0.8479 (p0) REVERT: C 87 PHE cc_start: 0.7565 (m-80) cc_final: 0.7053 (m-80) REVERT: D 757 MET cc_start: 0.8435 (mmm) cc_final: 0.8129 (mmm) REVERT: D 843 ASP cc_start: 0.8474 (m-30) cc_final: 0.8166 (m-30) REVERT: D 906 MET cc_start: 0.5916 (ppp) cc_final: 0.4928 (mtt) REVERT: D 938 LEU cc_start: 0.8899 (tp) cc_final: 0.8247 (tp) REVERT: D 999 ASN cc_start: 0.8492 (m-40) cc_final: 0.8018 (t0) REVERT: D 1008 MET cc_start: 0.8449 (mtm) cc_final: 0.8223 (tpp) REVERT: E 45 LEU cc_start: 0.8951 (tp) cc_final: 0.8602 (tp) REVERT: E 46 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8662 (tp30) REVERT: E 63 PHE cc_start: 0.8373 (m-80) cc_final: 0.7707 (m-10) REVERT: E 69 MET cc_start: 0.7865 (mtt) cc_final: 0.7521 (mtt) REVERT: E 86 ASP cc_start: 0.7684 (m-30) cc_final: 0.7483 (m-30) REVERT: E 100 MET cc_start: 0.6623 (pmm) cc_final: 0.6126 (pmm) REVERT: F 2 ILE cc_start: 0.9020 (mp) cc_final: 0.8005 (mm) REVERT: F 27 GLU cc_start: 0.8344 (tt0) cc_final: 0.8064 (tm-30) REVERT: F 38 GLN cc_start: 0.8399 (tt0) cc_final: 0.8025 (tt0) REVERT: F 42 GLN cc_start: 0.7553 (pt0) cc_final: 0.7330 (mp10) REVERT: F 80 GLU cc_start: 0.6912 (pm20) cc_final: 0.6535 (tm-30) REVERT: G 816 LYS cc_start: 0.7724 (tptt) cc_final: 0.7372 (tttt) REVERT: G 906 MET cc_start: 0.5235 (mmp) cc_final: 0.4394 (mmm) REVERT: G 913 MET cc_start: 0.4870 (ttp) cc_final: 0.4616 (ttp) REVERT: G 932 TYR cc_start: 0.6486 (m-10) cc_final: 0.6216 (m-10) REVERT: G 1177 ASN cc_start: 0.9145 (t0) cc_final: 0.8906 (t0) REVERT: H 31 ASP cc_start: 0.8315 (m-30) cc_final: 0.7563 (t70) REVERT: H 34 ILE cc_start: 0.9188 (tp) cc_final: 0.8840 (tp) REVERT: H 35 HIS cc_start: 0.8392 (m-70) cc_final: 0.7958 (m-70) REVERT: H 64 LYS cc_start: 0.7503 (mttt) cc_final: 0.7191 (tppt) REVERT: H 66 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7295 (mmt90) REVERT: H 68 THR cc_start: 0.9014 (t) cc_final: 0.8738 (p) REVERT: H 81 GLU cc_start: 0.9153 (mp0) cc_final: 0.8891 (mp0) REVERT: I 18 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8333 (mpp-170) REVERT: I 33 MET cc_start: 0.7707 (tpp) cc_final: 0.6868 (tpp) REVERT: I 35 TRP cc_start: 0.7319 (m100) cc_final: 0.6906 (m100) REVERT: I 36 PHE cc_start: 0.9204 (m-80) cc_final: 0.8438 (m-80) REVERT: I 42 GLN cc_start: 0.8342 (pt0) cc_final: 0.8058 (mm-40) REVERT: I 47 LEU cc_start: 0.7390 (mt) cc_final: 0.7180 (mm) REVERT: I 73 LEU cc_start: 0.8816 (tp) cc_final: 0.8392 (tp) REVERT: I 96 ARG cc_start: 0.7044 (mmm-85) cc_final: 0.6659 (mmm-85) REVERT: I 102 THR cc_start: 0.6976 (p) cc_final: 0.6734 (t) REVERT: J 71 TYR cc_start: 0.7884 (t80) cc_final: 0.7352 (t80) REVERT: J 75 PHE cc_start: 0.8576 (m-80) cc_final: 0.8189 (m-80) REVERT: J 171 LEU cc_start: 0.9327 (pp) cc_final: 0.9092 (pp) REVERT: J 287 TYR cc_start: 0.7657 (p90) cc_final: 0.7446 (p90) REVERT: J 288 ASP cc_start: 0.7682 (m-30) cc_final: 0.6836 (t0) REVERT: J 389 LEU cc_start: 0.7756 (mt) cc_final: 0.7302 (pp) REVERT: J 617 PHE cc_start: 0.7894 (m-80) cc_final: 0.7593 (m-10) REVERT: J 651 LEU cc_start: 0.9255 (tp) cc_final: 0.9039 (tp) REVERT: J 726 ASP cc_start: 0.7449 (t0) cc_final: 0.7123 (p0) REVERT: K 56 ILE cc_start: 0.9514 (mm) cc_final: 0.9281 (mm) REVERT: K 318 LEU cc_start: 0.8854 (mt) cc_final: 0.8621 (mt) REVERT: K 452 MET cc_start: 0.5434 (mmm) cc_final: 0.5047 (ttt) REVERT: L 36 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7247 (mp10) REVERT: L 56 ILE cc_start: 0.9521 (mm) cc_final: 0.9280 (pt) REVERT: L 169 LEU cc_start: 0.9512 (tt) cc_final: 0.9245 (tt) REVERT: L 240 MET cc_start: 0.7679 (ttt) cc_final: 0.7461 (tmm) REVERT: L 277 ASN cc_start: 0.8719 (m-40) cc_final: 0.8435 (m110) REVERT: L 296 ILE cc_start: 0.8525 (mm) cc_final: 0.8195 (mm) REVERT: L 324 LEU cc_start: 0.9296 (mm) cc_final: 0.9051 (mm) REVERT: L 563 MET cc_start: 0.7575 (ptm) cc_final: 0.6734 (tmm) REVERT: L 637 ASN cc_start: 0.8071 (m-40) cc_final: 0.7694 (m110) REVERT: L 729 LEU cc_start: 0.9384 (mt) cc_final: 0.9119 (mt) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.2102 time to fit residues: 188.6090 Evaluate side-chains 381 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 323 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 354 optimal weight: 0.0970 chunk 393 optimal weight: 40.0000 chunk 243 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN C 37 GLN C 90 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN G 974 GLN G1104 ASN G1212 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS J 236 ASN J 277 ASN J 619 ASN K 125 ASN K 421 ASN L 125 ASN L 236 ASN L 346 GLN L 637 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.086375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066688 restraints weight = 192552.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067878 restraints weight = 128114.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067832 restraints weight = 106228.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.068539 restraints weight = 83720.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068885 restraints weight = 69102.796| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33702 Z= 0.221 Angle : 0.705 10.778 45860 Z= 0.387 Chirality : 0.045 0.214 5075 Planarity : 0.006 0.088 5942 Dihedral : 5.474 28.954 4616 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.59 % Rotamer: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 0.69 (0.13), residues: 4214 helix: 0.90 (0.19), residues: 703 sheet: 0.30 (0.15), residues: 1037 loop : 0.55 (0.13), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 119 TYR 0.035 0.002 TYR G 905 PHE 0.036 0.002 PHE J 101 TRP 0.017 0.002 TRP B 36 HIS 0.009 0.002 HIS D1138 Details of bonding type rmsd covalent geometry : bond 0.00477 (33645) covalent geometry : angle 0.70290 (45746) SS BOND : bond 0.00528 ( 57) SS BOND : angle 1.39349 ( 114) hydrogen bonds : bond 0.05543 ( 1257) hydrogen bonds : angle 6.28990 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8866 (t80) cc_final: 0.8574 (t80) REVERT: A 805 ASP cc_start: 0.8762 (t0) cc_final: 0.7641 (m-30) REVERT: A 891 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7931 (mt-10) REVERT: A 978 TYR cc_start: 0.8293 (t80) cc_final: 0.8089 (t80) REVERT: A 980 LEU cc_start: 0.9616 (mt) cc_final: 0.9411 (mm) REVERT: B 5 GLN cc_start: 0.8303 (tp-100) cc_final: 0.7620 (mp10) REVERT: B 6 GLN cc_start: 0.6289 (tp-100) cc_final: 0.6053 (tp40) REVERT: B 59 TYR cc_start: 0.5759 (m-80) cc_final: 0.5492 (m-80) REVERT: B 60 ASN cc_start: 0.7930 (t0) cc_final: 0.7616 (t0) REVERT: B 72 ASP cc_start: 0.8474 (t0) cc_final: 0.8211 (t0) REVERT: B 76 SER cc_start: 0.9352 (m) cc_final: 0.8999 (p) REVERT: B 80 MET cc_start: 0.7305 (mtp) cc_final: 0.7087 (mtm) REVERT: B 81 GLU cc_start: 0.8389 (tt0) cc_final: 0.7709 (tp30) REVERT: B 82 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7402 (mtm180) REVERT: C 28 TYR cc_start: 0.8306 (m-80) cc_final: 0.8091 (m-80) REVERT: C 42 GLN cc_start: 0.7814 (pt0) cc_final: 0.7276 (mp10) REVERT: C 62 PHE cc_start: 0.8104 (m-80) cc_final: 0.7306 (m-80) REVERT: C 85 MET cc_start: 0.8323 (tpt) cc_final: 0.7863 (tpp) REVERT: C 87 PHE cc_start: 0.7579 (m-80) cc_final: 0.7067 (m-10) REVERT: D 757 MET cc_start: 0.8394 (mmm) cc_final: 0.8064 (mmt) REVERT: D 843 ASP cc_start: 0.8448 (m-30) cc_final: 0.8246 (m-30) REVERT: D 999 ASN cc_start: 0.8553 (m-40) cc_final: 0.8008 (t0) REVERT: D 1001 PHE cc_start: 0.9133 (t80) cc_final: 0.8741 (t80) REVERT: D 1169 ASN cc_start: 0.8284 (t0) cc_final: 0.7979 (t0) REVERT: E 20 ILE cc_start: 0.8569 (pt) cc_final: 0.8343 (pt) REVERT: E 80 MET cc_start: 0.8914 (mtp) cc_final: 0.8120 (ppp) REVERT: E 107 THR cc_start: 0.6308 (t) cc_final: 0.5951 (m) REVERT: F 2 ILE cc_start: 0.8976 (mp) cc_final: 0.8002 (mm) REVERT: F 11 LEU cc_start: 0.7839 (tp) cc_final: 0.7583 (pp) REVERT: F 27 GLU cc_start: 0.8309 (tt0) cc_final: 0.8036 (tm-30) REVERT: F 32 PHE cc_start: 0.8342 (m-80) cc_final: 0.8100 (m-80) REVERT: F 80 GLU cc_start: 0.6940 (pm20) cc_final: 0.6527 (tm-30) REVERT: G 816 LYS cc_start: 0.7647 (tptt) cc_final: 0.7328 (tttt) REVERT: G 906 MET cc_start: 0.5470 (mmp) cc_final: 0.4681 (mmm) REVERT: G 932 TYR cc_start: 0.6728 (m-10) cc_final: 0.6448 (m-10) REVERT: G 1104 ASN cc_start: 0.9478 (OUTLIER) cc_final: 0.8164 (t0) REVERT: G 1177 ASN cc_start: 0.9191 (t0) cc_final: 0.8977 (t0) REVERT: H 31 ASP cc_start: 0.8405 (m-30) cc_final: 0.8011 (t70) REVERT: H 34 ILE cc_start: 0.9187 (tp) cc_final: 0.8835 (tp) REVERT: H 66 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7245 (mmt90) REVERT: H 68 THR cc_start: 0.8934 (t) cc_final: 0.8683 (p) REVERT: H 81 GLU cc_start: 0.9140 (mp0) cc_final: 0.8861 (mp0) REVERT: I 18 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8228 (mpp-170) REVERT: I 33 MET cc_start: 0.7710 (tpp) cc_final: 0.7152 (tpp) REVERT: I 35 TRP cc_start: 0.7585 (m100) cc_final: 0.7255 (m100) REVERT: I 36 PHE cc_start: 0.9297 (m-80) cc_final: 0.8365 (m-80) REVERT: I 47 LEU cc_start: 0.7109 (mt) cc_final: 0.6735 (mm) REVERT: I 73 LEU cc_start: 0.8953 (tp) cc_final: 0.8532 (tp) REVERT: I 102 THR cc_start: 0.7049 (p) cc_final: 0.6804 (t) REVERT: J 71 TYR cc_start: 0.8009 (t80) cc_final: 0.7490 (t80) REVERT: J 240 MET cc_start: 0.7419 (tmm) cc_final: 0.7206 (tmm) REVERT: J 326 ASP cc_start: 0.8780 (t0) cc_final: 0.7541 (p0) REVERT: J 389 LEU cc_start: 0.7858 (mt) cc_final: 0.7278 (pp) REVERT: J 726 ASP cc_start: 0.7563 (t0) cc_final: 0.7217 (p0) REVERT: K 278 MET cc_start: 0.8437 (tpp) cc_final: 0.8172 (tpp) REVERT: K 452 MET cc_start: 0.5983 (mmm) cc_final: 0.5592 (ttt) REVERT: K 637 ASN cc_start: 0.8952 (t0) cc_final: 0.8715 (t0) REVERT: L 36 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7255 (mm-40) REVERT: L 56 ILE cc_start: 0.9577 (mm) cc_final: 0.9339 (mm) REVERT: L 148 MET cc_start: 0.7881 (tpp) cc_final: 0.7678 (tpp) REVERT: L 149 LEU cc_start: 0.9071 (mt) cc_final: 0.8637 (mt) REVERT: L 161 MET cc_start: 0.8812 (mpp) cc_final: 0.8573 (mpp) REVERT: L 277 ASN cc_start: 0.8760 (m-40) cc_final: 0.8227 (m110) REVERT: L 278 MET cc_start: 0.7784 (mpp) cc_final: 0.7572 (mpp) REVERT: L 324 LEU cc_start: 0.9245 (mm) cc_final: 0.9013 (mp) REVERT: L 563 MET cc_start: 0.7678 (ptm) cc_final: 0.7119 (tmm) REVERT: L 729 LEU cc_start: 0.9469 (mt) cc_final: 0.9170 (mt) outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.2058 time to fit residues: 153.2990 Evaluate side-chains 320 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 153 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 14 optimal weight: 0.0980 chunk 366 optimal weight: 30.0000 chunk 135 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 ASN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 974 GLN I 27DASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.086786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067028 restraints weight = 191641.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068714 restraints weight = 127518.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.069012 restraints weight = 84927.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.069361 restraints weight = 77368.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069426 restraints weight = 68840.988| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33702 Z= 0.155 Angle : 0.618 9.562 45860 Z= 0.336 Chirality : 0.044 0.199 5075 Planarity : 0.005 0.079 5942 Dihedral : 5.165 27.315 4616 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.89 % Favored : 95.89 % Rotamer: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 0.60 (0.13), residues: 4214 helix: 1.15 (0.20), residues: 713 sheet: 0.24 (0.15), residues: 1018 loop : 0.38 (0.13), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 61 TYR 0.024 0.001 TYR G 905 PHE 0.038 0.002 PHE J 101 TRP 0.014 0.002 TRP H 47 HIS 0.006 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00330 (33645) covalent geometry : angle 0.61526 (45746) SS BOND : bond 0.00608 ( 57) SS BOND : angle 1.37442 ( 114) hydrogen bonds : bond 0.04873 ( 1257) hydrogen bonds : angle 5.86242 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 435 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8737 (t80) cc_final: 0.8411 (t80) REVERT: A 805 ASP cc_start: 0.8800 (t0) cc_final: 0.7739 (m-30) REVERT: A 891 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 1058 LEU cc_start: 0.8219 (mt) cc_final: 0.7922 (mp) REVERT: B 4 LEU cc_start: 0.7312 (mt) cc_final: 0.6984 (mt) REVERT: B 5 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7682 (mp10) REVERT: B 6 GLN cc_start: 0.6351 (tp-100) cc_final: 0.6006 (tp40) REVERT: B 43 LYS cc_start: 0.8411 (tptt) cc_final: 0.8096 (tppt) REVERT: B 59 TYR cc_start: 0.5674 (m-80) cc_final: 0.5377 (m-80) REVERT: B 60 ASN cc_start: 0.7992 (t0) cc_final: 0.7618 (t0) REVERT: B 72 ASP cc_start: 0.8452 (t0) cc_final: 0.8154 (t0) REVERT: B 76 SER cc_start: 0.9366 (m) cc_final: 0.9145 (t) REVERT: B 81 GLU cc_start: 0.8414 (tt0) cc_final: 0.7791 (tp30) REVERT: B 82 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7442 (mtm180) REVERT: C 32 PHE cc_start: 0.6866 (m-10) cc_final: 0.6628 (m-10) REVERT: C 42 GLN cc_start: 0.7939 (pt0) cc_final: 0.7386 (mp10) REVERT: C 85 MET cc_start: 0.8539 (tpt) cc_final: 0.7968 (tpp) REVERT: C 87 PHE cc_start: 0.7503 (m-80) cc_final: 0.7136 (m-10) REVERT: D 757 MET cc_start: 0.8391 (mmm) cc_final: 0.8084 (mmt) REVERT: D 853 VAL cc_start: 0.7522 (t) cc_final: 0.7263 (t) REVERT: D 999 ASN cc_start: 0.8546 (m-40) cc_final: 0.7988 (t0) REVERT: D 1001 PHE cc_start: 0.9091 (t80) cc_final: 0.8670 (t80) REVERT: D 1169 ASN cc_start: 0.8376 (t0) cc_final: 0.8067 (t0) REVERT: E 20 ILE cc_start: 0.8495 (pt) cc_final: 0.8208 (pt) REVERT: E 45 LEU cc_start: 0.9101 (tp) cc_final: 0.8828 (tp) REVERT: E 46 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8787 (tp30) REVERT: E 60 ASN cc_start: 0.8453 (t0) cc_final: 0.8219 (p0) REVERT: E 80 MET cc_start: 0.8977 (mtp) cc_final: 0.8180 (ppp) REVERT: E 95 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7801 (ptmm) REVERT: E 107 THR cc_start: 0.6716 (t) cc_final: 0.6351 (m) REVERT: F 1 ASP cc_start: 0.8185 (p0) cc_final: 0.7916 (p0) REVERT: F 2 ILE cc_start: 0.8576 (mp) cc_final: 0.8009 (mm) REVERT: F 11 LEU cc_start: 0.7836 (tp) cc_final: 0.7591 (pp) REVERT: F 27 GLU cc_start: 0.8271 (tt0) cc_final: 0.7961 (tm-30) REVERT: F 32 PHE cc_start: 0.8203 (m-80) cc_final: 0.7883 (m-80) REVERT: F 80 GLU cc_start: 0.7063 (pm20) cc_final: 0.6745 (tm-30) REVERT: F 85 MET cc_start: 0.6337 (mmm) cc_final: 0.6121 (tpp) REVERT: F 97 THR cc_start: 0.9061 (t) cc_final: 0.8741 (p) REVERT: G 757 MET cc_start: 0.8205 (mpp) cc_final: 0.7228 (mpp) REVERT: G 816 LYS cc_start: 0.7652 (tptt) cc_final: 0.7331 (tttt) REVERT: G 906 MET cc_start: 0.5335 (mmp) cc_final: 0.4626 (mmm) REVERT: G 1104 ASN cc_start: 0.9287 (m-40) cc_final: 0.8406 (t0) REVERT: H 31 ASP cc_start: 0.8239 (m-30) cc_final: 0.8030 (t70) REVERT: H 34 ILE cc_start: 0.9182 (tp) cc_final: 0.8885 (tp) REVERT: H 66 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7034 (mmt90) REVERT: H 68 THR cc_start: 0.8887 (t) cc_final: 0.8653 (p) REVERT: H 81 GLU cc_start: 0.9132 (mp0) cc_final: 0.8848 (mp0) REVERT: I 18 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8297 (mpp-170) REVERT: I 27 VAL cc_start: 0.8664 (p) cc_final: 0.7770 (p) REVERT: I 33 MET cc_start: 0.7706 (tpp) cc_final: 0.6832 (tpp) REVERT: I 35 TRP cc_start: 0.7442 (m100) cc_final: 0.6626 (m100) REVERT: I 36 PHE cc_start: 0.9318 (m-80) cc_final: 0.8389 (m-80) REVERT: I 47 LEU cc_start: 0.6974 (mt) cc_final: 0.6676 (mm) REVERT: I 73 LEU cc_start: 0.9017 (tp) cc_final: 0.8564 (tp) REVERT: I 92 LYS cc_start: 0.9239 (tmtt) cc_final: 0.8559 (tptt) REVERT: I 102 THR cc_start: 0.7254 (p) cc_final: 0.6915 (t) REVERT: J 71 TYR cc_start: 0.7997 (t80) cc_final: 0.7481 (t80) REVERT: J 326 ASP cc_start: 0.8723 (t0) cc_final: 0.7573 (p0) REVERT: J 389 LEU cc_start: 0.7717 (mt) cc_final: 0.7089 (pp) REVERT: J 617 PHE cc_start: 0.8138 (m-80) cc_final: 0.7686 (m-10) REVERT: J 651 LEU cc_start: 0.9294 (tp) cc_final: 0.9081 (tp) REVERT: J 726 ASP cc_start: 0.7603 (t0) cc_final: 0.7186 (p0) REVERT: K 452 MET cc_start: 0.6127 (mmm) cc_final: 0.5669 (ttt) REVERT: K 637 ASN cc_start: 0.8980 (t0) cc_final: 0.8770 (t0) REVERT: K 696 MET cc_start: 0.5792 (mmp) cc_final: 0.5242 (mmm) REVERT: L 36 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7159 (mm-40) REVERT: L 56 ILE cc_start: 0.9585 (mm) cc_final: 0.9382 (mm) REVERT: L 116 PHE cc_start: 0.8081 (p90) cc_final: 0.7766 (p90) REVERT: L 149 LEU cc_start: 0.9077 (mt) cc_final: 0.8601 (mt) REVERT: L 161 MET cc_start: 0.8754 (mpp) cc_final: 0.8520 (mpp) REVERT: L 277 ASN cc_start: 0.8816 (m-40) cc_final: 0.8269 (m110) REVERT: L 563 MET cc_start: 0.7704 (ptm) cc_final: 0.7375 (tmm) REVERT: L 729 LEU cc_start: 0.9406 (mt) cc_final: 0.9165 (mt) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.2041 time to fit residues: 148.7162 Evaluate side-chains 325 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 12 optimal weight: 6.9990 chunk 396 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 chunk 159 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 53 optimal weight: 30.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN A 857 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 39 GLN D 792 GLN D 842 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1163 ASN J 421 ASN J 475 ASN K 193 ASN K 471 GLN L 167 HIS L 475 ASN L 576 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.081936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063317 restraints weight = 195645.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064287 restraints weight = 129905.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065792 restraints weight = 87708.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065473 restraints weight = 72589.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065069 restraints weight = 66986.859| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 33702 Z= 0.323 Angle : 0.846 13.318 45860 Z= 0.453 Chirality : 0.049 0.216 5075 Planarity : 0.006 0.073 5942 Dihedral : 6.038 39.265 4616 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.55 % Favored : 94.26 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4214 helix: 0.20 (0.19), residues: 698 sheet: -0.16 (0.15), residues: 1064 loop : -0.32 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 61 TYR 0.032 0.003 TYR A 794 PHE 0.030 0.003 PHE J 101 TRP 0.026 0.003 TRP D1184 HIS 0.012 0.002 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00697 (33645) covalent geometry : angle 0.84251 (45746) SS BOND : bond 0.00920 ( 57) SS BOND : angle 1.71170 ( 114) hydrogen bonds : bond 0.05868 ( 1257) hydrogen bonds : angle 6.62400 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 VAL cc_start: 0.9419 (t) cc_final: 0.9101 (m) REVERT: A 805 ASP cc_start: 0.8794 (t0) cc_final: 0.7724 (m-30) REVERT: A 857 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: A 891 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 1036 LEU cc_start: 0.9206 (tp) cc_final: 0.8662 (tp) REVERT: A 1084 GLN cc_start: 0.9300 (tm-30) cc_final: 0.9100 (tm-30) REVERT: B 60 ASN cc_start: 0.8124 (t0) cc_final: 0.7732 (t0) REVERT: B 72 ASP cc_start: 0.8505 (t0) cc_final: 0.8277 (t0) REVERT: B 80 MET cc_start: 0.7222 (mtp) cc_final: 0.6630 (mtp) REVERT: B 81 GLU cc_start: 0.8515 (tt0) cc_final: 0.7818 (tp30) REVERT: B 82 LEU cc_start: 0.7891 (pt) cc_final: 0.7676 (pt) REVERT: B 100 ASP cc_start: 0.8286 (m-30) cc_final: 0.8014 (m-30) REVERT: C 28 TYR cc_start: 0.8853 (m-80) cc_final: 0.8567 (m-80) REVERT: C 32 PHE cc_start: 0.7000 (m-10) cc_final: 0.6556 (m-10) REVERT: C 42 GLN cc_start: 0.7820 (pt0) cc_final: 0.7307 (mp10) REVERT: C 70 ASP cc_start: 0.8923 (t70) cc_final: 0.8629 (p0) REVERT: C 85 MET cc_start: 0.8569 (tpt) cc_final: 0.8035 (tpp) REVERT: C 86 TYR cc_start: 0.7611 (m-80) cc_final: 0.6747 (m-80) REVERT: C 87 PHE cc_start: 0.7358 (m-80) cc_final: 0.6776 (m-10) REVERT: D 757 MET cc_start: 0.8292 (mmm) cc_final: 0.8011 (mmt) REVERT: D 978 TYR cc_start: 0.8323 (t80) cc_final: 0.8114 (t80) REVERT: D 1001 PHE cc_start: 0.9173 (t80) cc_final: 0.8844 (t80) REVERT: E 41 HIS cc_start: 0.7312 (m90) cc_final: 0.7060 (m-70) REVERT: E 69 MET cc_start: 0.7351 (mmt) cc_final: 0.6739 (mmm) REVERT: E 72 ASP cc_start: 0.6011 (t0) cc_final: 0.5605 (t0) REVERT: E 95 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7668 (ptmt) REVERT: E 100 MET cc_start: 0.6860 (pmm) cc_final: 0.6076 (pmm) REVERT: E 107 THR cc_start: 0.6634 (t) cc_final: 0.6268 (m) REVERT: F 2 ILE cc_start: 0.8984 (mp) cc_final: 0.8440 (mm) REVERT: F 11 LEU cc_start: 0.8009 (tp) cc_final: 0.7776 (pp) REVERT: F 27 GLU cc_start: 0.8335 (tt0) cc_final: 0.7965 (tm-30) REVERT: F 32 PHE cc_start: 0.8462 (m-80) cc_final: 0.8161 (m-80) REVERT: F 33 MET cc_start: 0.8142 (mmm) cc_final: 0.7473 (mmm) REVERT: F 70 ASP cc_start: 0.8574 (t70) cc_final: 0.8343 (t0) REVERT: F 80 GLU cc_start: 0.7010 (pm20) cc_final: 0.6417 (tm-30) REVERT: G 816 LYS cc_start: 0.7851 (tptt) cc_final: 0.7507 (tptt) REVERT: G 906 MET cc_start: 0.5963 (mmp) cc_final: 0.5736 (mmp) REVERT: H 23 LYS cc_start: 0.9241 (tttt) cc_final: 0.8802 (ttpp) REVERT: H 34 ILE cc_start: 0.9386 (tp) cc_final: 0.9138 (tp) REVERT: H 35 HIS cc_start: 0.8069 (m170) cc_final: 0.7791 (m170) REVERT: H 69 MET cc_start: 0.8525 (mtm) cc_final: 0.8150 (mtm) REVERT: I 18 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8326 (mpp-170) REVERT: I 33 MET cc_start: 0.7925 (tpp) cc_final: 0.7718 (tpp) REVERT: I 35 TRP cc_start: 0.7620 (m100) cc_final: 0.7101 (m100) REVERT: I 36 PHE cc_start: 0.9296 (m-80) cc_final: 0.8158 (m-80) REVERT: I 73 LEU cc_start: 0.9074 (tp) cc_final: 0.8666 (tp) REVERT: I 93 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8571 (tm-30) REVERT: I 102 THR cc_start: 0.7612 (p) cc_final: 0.7107 (t) REVERT: J 71 TYR cc_start: 0.8280 (t80) cc_final: 0.7891 (t80) REVERT: J 726 ASP cc_start: 0.7772 (t0) cc_final: 0.7385 (p0) REVERT: K 278 MET cc_start: 0.8514 (tpp) cc_final: 0.8190 (tpp) REVERT: K 452 MET cc_start: 0.6188 (mmm) cc_final: 0.5703 (ttt) REVERT: K 637 ASN cc_start: 0.8958 (t0) cc_final: 0.8682 (t0) REVERT: L 149 LEU cc_start: 0.8879 (mt) cc_final: 0.8541 (mt) REVERT: L 161 MET cc_start: 0.8955 (mpp) cc_final: 0.8472 (mpp) REVERT: L 277 ASN cc_start: 0.8980 (m-40) cc_final: 0.8434 (m110) REVERT: L 278 MET cc_start: 0.8132 (mpp) cc_final: 0.7893 (mpp) REVERT: L 563 MET cc_start: 0.7767 (ptm) cc_final: 0.7420 (tmm) REVERT: L 648 TYR cc_start: 0.7743 (t80) cc_final: 0.7383 (t80) REVERT: L 729 LEU cc_start: 0.9459 (mt) cc_final: 0.9146 (mt) outliers start: 2 outliers final: 0 residues processed: 370 average time/residue: 0.1989 time to fit residues: 123.6905 Evaluate side-chains 287 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 23 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 291 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 356 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN A 857 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN D 974 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN F 38 GLN G 800 GLN G1104 ASN L 78 GLN L 167 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.083400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063104 restraints weight = 192350.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064219 restraints weight = 120447.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065019 restraints weight = 85909.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065615 restraints weight = 68615.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065939 restraints weight = 59219.075| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33702 Z= 0.189 Angle : 0.670 11.056 45860 Z= 0.362 Chirality : 0.045 0.212 5075 Planarity : 0.005 0.062 5942 Dihedral : 5.599 35.227 4616 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.05 % Favored : 94.76 % Rotamer: Outliers : 0.03 % Allowed : 1.76 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.25 (0.13), residues: 4214 helix: 0.60 (0.19), residues: 704 sheet: -0.21 (0.15), residues: 1094 loop : -0.29 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 921 TYR 0.026 0.002 TYR A 905 PHE 0.030 0.002 PHE J 101 TRP 0.029 0.002 TRP K 553 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00412 (33645) covalent geometry : angle 0.66618 (45746) SS BOND : bond 0.00408 ( 57) SS BOND : angle 1.58518 ( 114) hydrogen bonds : bond 0.05110 ( 1257) hydrogen bonds : angle 6.12240 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8797 (t80) cc_final: 0.8562 (t80) REVERT: A 804 VAL cc_start: 0.9351 (t) cc_final: 0.9022 (m) REVERT: A 805 ASP cc_start: 0.8817 (t0) cc_final: 0.7737 (m-30) REVERT: A 891 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 943 MET cc_start: 0.8755 (mmm) cc_final: 0.8522 (mmt) REVERT: A 1036 LEU cc_start: 0.9049 (tp) cc_final: 0.8511 (tp) REVERT: B 60 ASN cc_start: 0.8122 (t0) cc_final: 0.7769 (t0) REVERT: B 72 ASP cc_start: 0.8461 (t0) cc_final: 0.8179 (t0) REVERT: B 80 MET cc_start: 0.7465 (mtp) cc_final: 0.7089 (mtp) REVERT: B 81 GLU cc_start: 0.8609 (tt0) cc_final: 0.7927 (tp30) REVERT: B 82 LEU cc_start: 0.7929 (pt) cc_final: 0.7671 (pt) REVERT: B 82 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7224 (mtm180) REVERT: C 32 PHE cc_start: 0.6872 (m-10) cc_final: 0.6489 (m-10) REVERT: C 42 GLN cc_start: 0.7662 (pt0) cc_final: 0.7128 (mp10) REVERT: C 70 ASP cc_start: 0.8842 (t70) cc_final: 0.8601 (p0) REVERT: C 85 MET cc_start: 0.8645 (tpt) cc_final: 0.8261 (tpp) REVERT: C 87 PHE cc_start: 0.7311 (m-80) cc_final: 0.6825 (m-10) REVERT: D 843 ASP cc_start: 0.8206 (m-30) cc_final: 0.7988 (m-30) REVERT: D 978 TYR cc_start: 0.8131 (t80) cc_final: 0.7924 (t80) REVERT: D 999 ASN cc_start: 0.8596 (m-40) cc_final: 0.7996 (t0) REVERT: D 1001 PHE cc_start: 0.9005 (t80) cc_final: 0.8771 (t80) REVERT: E 34 ILE cc_start: 0.9697 (mm) cc_final: 0.9295 (tp) REVERT: E 41 HIS cc_start: 0.7426 (m90) cc_final: 0.6875 (m-70) REVERT: E 53 TYR cc_start: 0.8099 (t80) cc_final: 0.7849 (t80) REVERT: E 69 MET cc_start: 0.7287 (mmt) cc_final: 0.6756 (mmm) REVERT: E 72 ASP cc_start: 0.6139 (t0) cc_final: 0.5638 (t0) REVERT: E 100 MET cc_start: 0.6891 (pmm) cc_final: 0.6423 (pmm) REVERT: E 107 THR cc_start: 0.6755 (t) cc_final: 0.6318 (m) REVERT: F 2 ILE cc_start: 0.9072 (mp) cc_final: 0.8626 (mm) REVERT: F 27 GLU cc_start: 0.8296 (tt0) cc_final: 0.7969 (tm-30) REVERT: F 33 MET cc_start: 0.8138 (mmm) cc_final: 0.7684 (mmm) REVERT: F 36 PHE cc_start: 0.9151 (m-80) cc_final: 0.8927 (m-80) REVERT: F 80 GLU cc_start: 0.6948 (pm20) cc_final: 0.6576 (tm-30) REVERT: G 816 LYS cc_start: 0.7697 (tptt) cc_final: 0.7417 (tptt) REVERT: H 23 LYS cc_start: 0.9221 (tttt) cc_final: 0.8916 (ttpt) REVERT: H 35 HIS cc_start: 0.8007 (m170) cc_final: 0.7738 (m170) REVERT: H 62 LYS cc_start: 0.8410 (ptmm) cc_final: 0.8192 (ptpp) REVERT: H 81 GLU cc_start: 0.9005 (mp0) cc_final: 0.8793 (mp0) REVERT: I 18 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8314 (mpp-170) REVERT: I 33 MET cc_start: 0.7840 (tpp) cc_final: 0.7173 (tpp) REVERT: I 35 TRP cc_start: 0.7476 (m100) cc_final: 0.6535 (m100) REVERT: I 36 PHE cc_start: 0.9178 (m-80) cc_final: 0.8031 (m-80) REVERT: I 73 LEU cc_start: 0.9279 (tp) cc_final: 0.8993 (tp) REVERT: I 102 THR cc_start: 0.7474 (p) cc_final: 0.6975 (t) REVERT: J 71 TYR cc_start: 0.8243 (t80) cc_final: 0.7920 (t80) REVERT: J 326 ASP cc_start: 0.8820 (t0) cc_final: 0.8083 (p0) REVERT: K 278 MET cc_start: 0.8361 (tpp) cc_final: 0.8011 (tpp) REVERT: K 452 MET cc_start: 0.6237 (mmm) cc_final: 0.5802 (ttt) REVERT: K 637 ASN cc_start: 0.8915 (t0) cc_final: 0.8640 (t0) REVERT: L 149 LEU cc_start: 0.8980 (mt) cc_final: 0.8684 (mt) REVERT: L 161 MET cc_start: 0.8856 (mpp) cc_final: 0.8505 (mpp) REVERT: L 277 ASN cc_start: 0.9055 (m-40) cc_final: 0.8485 (m110) REVERT: L 563 MET cc_start: 0.7572 (ptm) cc_final: 0.7363 (tmm) REVERT: L 729 LEU cc_start: 0.9388 (mt) cc_final: 0.9161 (mt) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.1989 time to fit residues: 124.6645 Evaluate side-chains 293 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 220 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 403 optimal weight: 30.0000 chunk 260 optimal weight: 40.0000 chunk 17 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN C 53 ASN D 974 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1176 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN I 34 ASN ** K 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 ASN L 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.081622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061450 restraints weight = 195826.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062511 restraints weight = 124227.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063315 restraints weight = 88668.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063862 restraints weight = 70911.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064167 restraints weight = 61388.599| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 33702 Z= 0.258 Angle : 0.752 11.699 45860 Z= 0.405 Chirality : 0.047 0.347 5075 Planarity : 0.006 0.067 5942 Dihedral : 5.867 36.757 4616 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.50 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.60 (0.13), residues: 4214 helix: 0.34 (0.19), residues: 703 sheet: -0.37 (0.15), residues: 1095 loop : -0.57 (0.13), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 61 TYR 0.028 0.002 TYR G1186 PHE 0.028 0.003 PHE J 183 TRP 0.022 0.003 TRP D1184 HIS 0.009 0.002 HIS J 681 Details of bonding type rmsd covalent geometry : bond 0.00564 (33645) covalent geometry : angle 0.74882 (45746) SS BOND : bond 0.00567 ( 57) SS BOND : angle 1.64796 ( 114) hydrogen bonds : bond 0.05398 ( 1257) hydrogen bonds : angle 6.36302 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 804 VAL cc_start: 0.9406 (t) cc_final: 0.9158 (m) REVERT: A 891 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7913 (mt-10) REVERT: A 906 MET cc_start: 0.3678 (mmp) cc_final: 0.3477 (mmp) REVERT: A 1036 LEU cc_start: 0.9206 (tp) cc_final: 0.8724 (tp) REVERT: A 1059 ASP cc_start: 0.8482 (t70) cc_final: 0.8163 (t70) REVERT: B 41 HIS cc_start: 0.8237 (t-90) cc_final: 0.7479 (m90) REVERT: B 60 ASN cc_start: 0.8052 (t0) cc_final: 0.7716 (t0) REVERT: B 72 ASP cc_start: 0.8556 (t0) cc_final: 0.8306 (t0) REVERT: B 80 MET cc_start: 0.7584 (mtp) cc_final: 0.7292 (mtm) REVERT: B 81 GLU cc_start: 0.8673 (tt0) cc_final: 0.7950 (tp30) REVERT: B 82 LEU cc_start: 0.7974 (pt) cc_final: 0.7748 (pt) REVERT: B 82 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7211 (mtm180) REVERT: C 32 PHE cc_start: 0.6793 (m-10) cc_final: 0.6393 (m-10) REVERT: C 42 GLN cc_start: 0.7763 (pt0) cc_final: 0.7227 (mp10) REVERT: C 62 PHE cc_start: 0.7869 (m-10) cc_final: 0.7539 (m-80) REVERT: C 70 ASP cc_start: 0.8849 (t70) cc_final: 0.8582 (p0) REVERT: C 85 MET cc_start: 0.8578 (tpt) cc_final: 0.8255 (tpp) REVERT: D 757 MET cc_start: 0.8118 (mmm) cc_final: 0.7730 (mmm) REVERT: D 843 ASP cc_start: 0.8252 (m-30) cc_final: 0.8038 (m-30) REVERT: D 978 TYR cc_start: 0.8154 (t80) cc_final: 0.7950 (t80) REVERT: D 999 ASN cc_start: 0.8618 (m-40) cc_final: 0.7781 (t0) REVERT: D 1001 PHE cc_start: 0.9081 (t80) cc_final: 0.8795 (t80) REVERT: E 41 HIS cc_start: 0.7321 (m90) cc_final: 0.7045 (m-70) REVERT: E 69 MET cc_start: 0.7233 (mmt) cc_final: 0.6808 (mmm) REVERT: E 72 ASP cc_start: 0.5884 (t0) cc_final: 0.5369 (t0) REVERT: E 95 LYS cc_start: 0.8112 (ptmm) cc_final: 0.7806 (ptmm) REVERT: E 107 THR cc_start: 0.6674 (t) cc_final: 0.6263 (m) REVERT: F 2 ILE cc_start: 0.8981 (mp) cc_final: 0.8544 (mm) REVERT: F 27 GLU cc_start: 0.8249 (tt0) cc_final: 0.7833 (tm-30) REVERT: F 80 GLU cc_start: 0.7032 (pm20) cc_final: 0.6625 (tm-30) REVERT: F 82 ASP cc_start: 0.7513 (m-30) cc_final: 0.7284 (m-30) REVERT: G 816 LYS cc_start: 0.7846 (tptt) cc_final: 0.7592 (tttt) REVERT: G 1024 ASP cc_start: 0.8643 (m-30) cc_final: 0.8322 (t0) REVERT: H 23 LYS cc_start: 0.9318 (tttt) cc_final: 0.9069 (ttpt) REVERT: H 31 ASP cc_start: 0.8355 (t70) cc_final: 0.8087 (t70) REVERT: H 35 HIS cc_start: 0.7968 (m170) cc_final: 0.7710 (m170) REVERT: H 81 GLU cc_start: 0.9021 (mp0) cc_final: 0.8567 (mp0) REVERT: I 18 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8436 (ttp80) REVERT: I 33 MET cc_start: 0.7935 (tpp) cc_final: 0.7309 (tpp) REVERT: I 35 TRP cc_start: 0.7652 (m100) cc_final: 0.6449 (m-10) REVERT: I 36 PHE cc_start: 0.9126 (m-80) cc_final: 0.8044 (m-80) REVERT: I 102 THR cc_start: 0.7677 (p) cc_final: 0.7170 (t) REVERT: J 71 TYR cc_start: 0.8401 (t80) cc_final: 0.8003 (t80) REVERT: J 326 ASP cc_start: 0.8929 (t0) cc_final: 0.8113 (p0) REVERT: K 278 MET cc_start: 0.8459 (tpp) cc_final: 0.8133 (tpp) REVERT: K 452 MET cc_start: 0.6227 (mmm) cc_final: 0.5805 (ttt) REVERT: K 629 ARG cc_start: 0.7233 (mmp80) cc_final: 0.6532 (mtp-110) REVERT: K 637 ASN cc_start: 0.8966 (t0) cc_final: 0.8683 (t0) REVERT: L 149 LEU cc_start: 0.8899 (mt) cc_final: 0.8418 (mt) REVERT: L 161 MET cc_start: 0.8994 (mpp) cc_final: 0.8588 (mpp) REVERT: L 277 ASN cc_start: 0.9084 (m-40) cc_final: 0.8550 (m110) REVERT: L 324 LEU cc_start: 0.9289 (mt) cc_final: 0.8805 (mp) REVERT: L 496 LYS cc_start: 0.1858 (ptpt) cc_final: 0.1624 (ptpt) REVERT: L 648 TYR cc_start: 0.7540 (t80) cc_final: 0.7200 (t80) REVERT: L 729 LEU cc_start: 0.9469 (mt) cc_final: 0.9191 (mt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1937 time to fit residues: 115.1633 Evaluate side-chains 276 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 378 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 172 optimal weight: 0.0980 chunk 205 optimal weight: 10.0000 chunk 394 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 318 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN D 974 GLN D1104 ASN D1132 ASN G 927 GLN G1063 GLN K 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.083292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064494 restraints weight = 192585.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065287 restraints weight = 125407.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065367 restraints weight = 106060.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066011 restraints weight = 85603.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066284 restraints weight = 67655.665| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33702 Z= 0.152 Angle : 0.642 11.653 45860 Z= 0.346 Chirality : 0.045 0.334 5075 Planarity : 0.005 0.108 5942 Dihedral : 5.460 31.776 4616 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.38 (0.13), residues: 4214 helix: 0.73 (0.20), residues: 717 sheet: -0.28 (0.15), residues: 1061 loop : -0.48 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 66 TYR 0.028 0.002 TYR A 905 PHE 0.028 0.002 PHE E 29 TRP 0.018 0.002 TRP H 47 HIS 0.005 0.001 HIS L 348 Details of bonding type rmsd covalent geometry : bond 0.00334 (33645) covalent geometry : angle 0.63715 (45746) SS BOND : bond 0.00378 ( 57) SS BOND : angle 1.64024 ( 114) hydrogen bonds : bond 0.04826 ( 1257) hydrogen bonds : angle 5.90366 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8779 (t80) cc_final: 0.8519 (t80) REVERT: A 804 VAL cc_start: 0.9414 (t) cc_final: 0.9170 (m) REVERT: A 816 LYS cc_start: 0.8890 (tptt) cc_final: 0.8512 (mttp) REVERT: A 906 MET cc_start: 0.3664 (mmp) cc_final: 0.3419 (mmp) REVERT: A 1036 LEU cc_start: 0.9173 (tp) cc_final: 0.8666 (tp) REVERT: B 60 ASN cc_start: 0.8129 (t0) cc_final: 0.7745 (t0) REVERT: B 72 ASP cc_start: 0.8683 (t0) cc_final: 0.8417 (t0) REVERT: B 80 MET cc_start: 0.7501 (mtp) cc_final: 0.7287 (mtm) REVERT: B 81 GLU cc_start: 0.8675 (tt0) cc_final: 0.8003 (tp30) REVERT: B 82 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7165 (mtm180) REVERT: C 32 PHE cc_start: 0.6637 (m-10) cc_final: 0.6277 (m-10) REVERT: C 42 GLN cc_start: 0.7785 (pt0) cc_final: 0.7242 (mp10) REVERT: C 62 PHE cc_start: 0.8097 (m-10) cc_final: 0.7813 (m-80) REVERT: C 87 PHE cc_start: 0.7129 (m-80) cc_final: 0.6108 (m-10) REVERT: D 757 MET cc_start: 0.8165 (mmm) cc_final: 0.7867 (mmm) REVERT: D 843 ASP cc_start: 0.8249 (m-30) cc_final: 0.8023 (m-30) REVERT: D 999 ASN cc_start: 0.8571 (m-40) cc_final: 0.7746 (t0) REVERT: D 1001 PHE cc_start: 0.9024 (t80) cc_final: 0.8781 (t80) REVERT: D 1132 ASN cc_start: 0.8782 (m-40) cc_final: 0.8567 (m-40) REVERT: E 34 ILE cc_start: 0.9747 (mm) cc_final: 0.9377 (tp) REVERT: E 41 HIS cc_start: 0.7562 (m90) cc_final: 0.7294 (m-70) REVERT: E 63 PHE cc_start: 0.8364 (m-80) cc_final: 0.8095 (m-80) REVERT: E 69 MET cc_start: 0.7134 (mmt) cc_final: 0.6726 (mmm) REVERT: E 72 ASP cc_start: 0.5833 (t0) cc_final: 0.5330 (t0) REVERT: E 80 MET cc_start: 0.8616 (mtp) cc_final: 0.8199 (tmm) REVERT: E 107 THR cc_start: 0.6481 (t) cc_final: 0.6126 (m) REVERT: F 2 ILE cc_start: 0.8946 (mp) cc_final: 0.8438 (mm) REVERT: F 27 GLU cc_start: 0.8298 (tt0) cc_final: 0.7969 (tm-30) REVERT: F 34 ASN cc_start: 0.8549 (m110) cc_final: 0.8300 (m110) REVERT: F 70 ASP cc_start: 0.8432 (t70) cc_final: 0.8224 (t0) REVERT: F 80 GLU cc_start: 0.7100 (pm20) cc_final: 0.6769 (tm-30) REVERT: G 816 LYS cc_start: 0.7811 (tptt) cc_final: 0.7590 (tttt) REVERT: G 1222 LEU cc_start: 0.8512 (tp) cc_final: 0.8267 (pt) REVERT: H 23 LYS cc_start: 0.9302 (tttt) cc_final: 0.9058 (ttpt) REVERT: H 31 ASP cc_start: 0.8323 (t70) cc_final: 0.8069 (t70) REVERT: H 34 ILE cc_start: 0.9342 (tp) cc_final: 0.9141 (tp) REVERT: H 35 HIS cc_start: 0.7960 (m170) cc_final: 0.7623 (m170) REVERT: H 81 GLU cc_start: 0.9018 (mp0) cc_final: 0.8776 (mp0) REVERT: I 18 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8523 (ttp80) REVERT: I 33 MET cc_start: 0.7837 (tpp) cc_final: 0.7191 (tpp) REVERT: I 35 TRP cc_start: 0.7622 (m100) cc_final: 0.6633 (m-10) REVERT: I 36 PHE cc_start: 0.9270 (m-80) cc_final: 0.8116 (m-10) REVERT: I 102 THR cc_start: 0.7404 (p) cc_final: 0.6958 (t) REVERT: J 71 TYR cc_start: 0.8382 (t80) cc_final: 0.7949 (t80) REVERT: J 116 PHE cc_start: 0.8705 (p90) cc_final: 0.7721 (p90) REVERT: J 326 ASP cc_start: 0.8801 (t0) cc_final: 0.8166 (p0) REVERT: J 476 PRO cc_start: 0.5395 (Cg_endo) cc_final: 0.5178 (Cg_exo) REVERT: J 651 LEU cc_start: 0.9327 (tp) cc_final: 0.9118 (mt) REVERT: K 172 LEU cc_start: 0.9014 (pt) cc_final: 0.8154 (tp) REVERT: K 180 LEU cc_start: 0.9299 (tp) cc_final: 0.9074 (tp) REVERT: K 278 MET cc_start: 0.8339 (tpp) cc_final: 0.7976 (tpp) REVERT: K 400 LYS cc_start: 0.5065 (mttt) cc_final: 0.4822 (mttp) REVERT: K 452 MET cc_start: 0.6181 (mmm) cc_final: 0.5756 (ttt) REVERT: K 629 ARG cc_start: 0.7208 (mmp80) cc_final: 0.6452 (mtp-110) REVERT: K 637 ASN cc_start: 0.8888 (t0) cc_final: 0.8624 (t0) REVERT: L 149 LEU cc_start: 0.9028 (mt) cc_final: 0.8552 (mt) REVERT: L 161 MET cc_start: 0.8965 (mpp) cc_final: 0.8668 (mpp) REVERT: L 277 ASN cc_start: 0.9112 (m-40) cc_final: 0.8624 (m110) REVERT: L 602 ASN cc_start: 0.7918 (p0) cc_final: 0.7546 (p0) REVERT: L 696 MET cc_start: 0.6365 (pmm) cc_final: 0.6052 (pmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1910 time to fit residues: 119.5503 Evaluate side-chains 291 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 59 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 263 optimal weight: 6.9990 chunk 197 optimal weight: 0.0570 chunk 89 optimal weight: 8.9990 chunk 321 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 386 optimal weight: 20.0000 chunk 301 optimal weight: 30.0000 overall best weight: 2.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.083671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065337 restraints weight = 192650.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066306 restraints weight = 127784.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066133 restraints weight = 91178.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.066335 restraints weight = 92501.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066425 restraints weight = 82534.648| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33702 Z= 0.143 Angle : 0.629 10.525 45860 Z= 0.338 Chirality : 0.044 0.267 5075 Planarity : 0.005 0.103 5942 Dihedral : 5.241 31.952 4616 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.77 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.27 (0.13), residues: 4214 helix: 0.96 (0.20), residues: 719 sheet: -0.19 (0.15), residues: 1054 loop : -0.47 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 66 TYR 0.027 0.002 TYR A 905 PHE 0.027 0.002 PHE E 29 TRP 0.018 0.002 TRP H 47 HIS 0.004 0.001 HIS L 194 Details of bonding type rmsd covalent geometry : bond 0.00310 (33645) covalent geometry : angle 0.62435 (45746) SS BOND : bond 0.00345 ( 57) SS BOND : angle 1.64877 ( 114) hydrogen bonds : bond 0.04598 ( 1257) hydrogen bonds : angle 5.71764 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8695 (t80) cc_final: 0.8414 (t80) REVERT: A 804 VAL cc_start: 0.9343 (t) cc_final: 0.9067 (m) REVERT: A 816 LYS cc_start: 0.8902 (tptt) cc_final: 0.8546 (mttp) REVERT: A 906 MET cc_start: 0.3773 (mmp) cc_final: 0.3521 (mmp) REVERT: A 1036 LEU cc_start: 0.9155 (tp) cc_final: 0.8715 (tp) REVERT: B 43 LYS cc_start: 0.8571 (tptt) cc_final: 0.7773 (tppt) REVERT: B 60 ASN cc_start: 0.8123 (t0) cc_final: 0.7776 (t0) REVERT: B 72 ASP cc_start: 0.8661 (t0) cc_final: 0.8406 (t0) REVERT: B 81 GLU cc_start: 0.8664 (tt0) cc_final: 0.7938 (tp30) REVERT: B 82 LEU cc_start: 0.7854 (pt) cc_final: 0.7530 (pt) REVERT: B 82 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7113 (mtm180) REVERT: C 32 PHE cc_start: 0.6626 (m-10) cc_final: 0.6377 (m-10) REVERT: C 42 GLN cc_start: 0.7746 (pt0) cc_final: 0.7233 (mp10) REVERT: C 62 PHE cc_start: 0.7978 (m-10) cc_final: 0.7576 (m-80) REVERT: C 85 MET cc_start: 0.8514 (tpt) cc_final: 0.8214 (tpp) REVERT: C 87 PHE cc_start: 0.7111 (m-80) cc_final: 0.5976 (m-10) REVERT: D 757 MET cc_start: 0.8252 (mmm) cc_final: 0.7912 (mmm) REVERT: D 978 TYR cc_start: 0.8146 (t80) cc_final: 0.7936 (t80) REVERT: D 999 ASN cc_start: 0.8590 (m-40) cc_final: 0.8002 (t0) REVERT: D 1001 PHE cc_start: 0.8980 (t80) cc_final: 0.8636 (t80) REVERT: D 1132 ASN cc_start: 0.8833 (m-40) cc_final: 0.8582 (m-40) REVERT: E 34 ILE cc_start: 0.9759 (mm) cc_final: 0.9387 (tp) REVERT: E 41 HIS cc_start: 0.7495 (m90) cc_final: 0.7196 (m170) REVERT: E 69 MET cc_start: 0.7212 (mmt) cc_final: 0.6868 (mmm) REVERT: E 72 ASP cc_start: 0.6043 (t0) cc_final: 0.5550 (t70) REVERT: E 80 MET cc_start: 0.8584 (mtp) cc_final: 0.8302 (tmm) REVERT: E 107 THR cc_start: 0.6362 (t) cc_final: 0.5943 (m) REVERT: F 2 ILE cc_start: 0.8884 (mp) cc_final: 0.8457 (mm) REVERT: F 27 GLU cc_start: 0.8278 (tt0) cc_final: 0.8065 (tm-30) REVERT: F 80 GLU cc_start: 0.7277 (pm20) cc_final: 0.7008 (tm-30) REVERT: F 82 ASP cc_start: 0.7252 (m-30) cc_final: 0.7041 (m-30) REVERT: G 1222 LEU cc_start: 0.8443 (tp) cc_final: 0.8203 (pt) REVERT: H 23 LYS cc_start: 0.9311 (tttt) cc_final: 0.9050 (ttpt) REVERT: H 31 ASP cc_start: 0.8317 (t70) cc_final: 0.8082 (t70) REVERT: H 35 HIS cc_start: 0.8020 (m170) cc_final: 0.7700 (m170) REVERT: H 81 GLU cc_start: 0.8973 (mp0) cc_final: 0.8721 (mp0) REVERT: I 18 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8510 (ttp80) REVERT: I 33 MET cc_start: 0.7883 (tpp) cc_final: 0.7332 (tpp) REVERT: I 36 PHE cc_start: 0.9276 (m-80) cc_final: 0.8126 (m-10) REVERT: I 102 THR cc_start: 0.7478 (p) cc_final: 0.7032 (t) REVERT: J 71 TYR cc_start: 0.8380 (t80) cc_final: 0.7939 (t80) REVERT: J 116 PHE cc_start: 0.8620 (p90) cc_final: 0.7967 (p90) REVERT: J 171 LEU cc_start: 0.9321 (pp) cc_final: 0.9018 (pp) REVERT: J 326 ASP cc_start: 0.8778 (t0) cc_final: 0.8193 (p0) REVERT: J 476 PRO cc_start: 0.5168 (Cg_endo) cc_final: 0.4908 (Cg_exo) REVERT: J 617 PHE cc_start: 0.8297 (m-80) cc_final: 0.7854 (m-10) REVERT: K 172 LEU cc_start: 0.8996 (pt) cc_final: 0.8216 (tp) REVERT: K 278 MET cc_start: 0.8372 (tpp) cc_final: 0.8005 (tpp) REVERT: K 415 LEU cc_start: 0.5643 (tp) cc_final: 0.5129 (pp) REVERT: K 452 MET cc_start: 0.6196 (mmm) cc_final: 0.5770 (ttt) REVERT: K 637 ASN cc_start: 0.8896 (t0) cc_final: 0.8614 (t0) REVERT: L 149 LEU cc_start: 0.8965 (mt) cc_final: 0.8492 (mt) REVERT: L 161 MET cc_start: 0.8881 (mpp) cc_final: 0.8623 (mpp) REVERT: L 277 ASN cc_start: 0.9140 (m-40) cc_final: 0.8617 (m110) REVERT: L 602 ASN cc_start: 0.7923 (p0) cc_final: 0.7481 (p0) REVERT: L 696 MET cc_start: 0.6186 (pmm) cc_final: 0.5884 (pmm) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1970 time to fit residues: 122.8454 Evaluate side-chains 297 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 350 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 413 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 522 GLN ** L 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 681 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.083034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.064445 restraints weight = 193854.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.065552 restraints weight = 131913.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065420 restraints weight = 94122.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065613 restraints weight = 87051.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065758 restraints weight = 86167.964| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33702 Z= 0.173 Angle : 0.650 10.575 45860 Z= 0.350 Chirality : 0.044 0.239 5075 Planarity : 0.005 0.096 5942 Dihedral : 5.295 31.146 4616 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.15 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.13), residues: 4214 helix: 0.86 (0.20), residues: 719 sheet: -0.25 (0.15), residues: 1045 loop : -0.52 (0.13), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 94 TYR 0.026 0.002 TYR A 905 PHE 0.028 0.002 PHE E 29 TRP 0.015 0.002 TRP A 960 HIS 0.004 0.001 HIS J 194 Details of bonding type rmsd covalent geometry : bond 0.00378 (33645) covalent geometry : angle 0.64563 (45746) SS BOND : bond 0.00381 ( 57) SS BOND : angle 1.60753 ( 114) hydrogen bonds : bond 0.04644 ( 1257) hydrogen bonds : angle 5.80623 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 TYR cc_start: 0.8694 (t80) cc_final: 0.8443 (t80) REVERT: A 804 VAL cc_start: 0.9362 (t) cc_final: 0.9092 (m) REVERT: A 816 LYS cc_start: 0.8908 (tptt) cc_final: 0.8574 (mttp) REVERT: A 906 MET cc_start: 0.3798 (mmp) cc_final: 0.3574 (mmp) REVERT: A 1036 LEU cc_start: 0.9155 (tp) cc_final: 0.8682 (tp) REVERT: B 43 LYS cc_start: 0.8646 (tptt) cc_final: 0.7843 (tppt) REVERT: B 60 ASN cc_start: 0.8126 (t0) cc_final: 0.7804 (t0) REVERT: B 72 ASP cc_start: 0.8655 (t0) cc_final: 0.8381 (t0) REVERT: B 81 GLU cc_start: 0.8568 (tt0) cc_final: 0.7894 (tp30) REVERT: B 82 LEU cc_start: 0.7743 (pt) cc_final: 0.7425 (pt) REVERT: C 27 GLU cc_start: 0.8295 (tt0) cc_final: 0.7973 (mp0) REVERT: C 32 PHE cc_start: 0.6518 (m-10) cc_final: 0.6297 (m-10) REVERT: C 42 GLN cc_start: 0.7760 (pt0) cc_final: 0.7293 (mp10) REVERT: C 62 PHE cc_start: 0.8040 (m-10) cc_final: 0.7637 (m-80) REVERT: C 85 MET cc_start: 0.8504 (tpt) cc_final: 0.8200 (tpp) REVERT: C 87 PHE cc_start: 0.7008 (m-80) cc_final: 0.5991 (m-10) REVERT: D 757 MET cc_start: 0.8260 (mmm) cc_final: 0.7935 (mmm) REVERT: D 978 TYR cc_start: 0.8107 (t80) cc_final: 0.7894 (t80) REVERT: D 999 ASN cc_start: 0.8593 (m-40) cc_final: 0.7990 (t0) REVERT: D 1001 PHE cc_start: 0.9005 (t80) cc_final: 0.8676 (t80) REVERT: E 34 ILE cc_start: 0.9735 (mm) cc_final: 0.9350 (tp) REVERT: E 41 HIS cc_start: 0.7528 (m90) cc_final: 0.7224 (m-70) REVERT: E 53 TYR cc_start: 0.8544 (t80) cc_final: 0.8092 (t80) REVERT: E 69 MET cc_start: 0.7107 (mmt) cc_final: 0.6796 (mmm) REVERT: E 72 ASP cc_start: 0.5857 (t0) cc_final: 0.5364 (t70) REVERT: E 80 MET cc_start: 0.8604 (mtp) cc_final: 0.8311 (tmm) REVERT: E 107 THR cc_start: 0.6326 (t) cc_final: 0.5906 (m) REVERT: F 2 ILE cc_start: 0.8775 (mp) cc_final: 0.8284 (mm) REVERT: F 27 GLU cc_start: 0.8303 (tt0) cc_final: 0.8057 (tm-30) REVERT: F 80 GLU cc_start: 0.7371 (pm20) cc_final: 0.7119 (tm-30) REVERT: F 85 MET cc_start: 0.6777 (tpt) cc_final: 0.6267 (mmm) REVERT: G 1222 LEU cc_start: 0.8439 (tp) cc_final: 0.8173 (pt) REVERT: H 23 LYS cc_start: 0.9263 (tttt) cc_final: 0.9040 (ttpt) REVERT: H 31 ASP cc_start: 0.8378 (t70) cc_final: 0.8133 (t70) REVERT: H 34 ILE cc_start: 0.9362 (tp) cc_final: 0.9148 (tp) REVERT: H 35 HIS cc_start: 0.8082 (m170) cc_final: 0.7687 (m170) REVERT: H 81 GLU cc_start: 0.8991 (mp0) cc_final: 0.8736 (mp0) REVERT: I 15 LEU cc_start: 0.8528 (mm) cc_final: 0.8142 (mm) REVERT: I 18 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8524 (ttp80) REVERT: I 33 MET cc_start: 0.7824 (tpp) cc_final: 0.7241 (tpp) REVERT: I 36 PHE cc_start: 0.9296 (m-80) cc_final: 0.8253 (m-10) REVERT: I 102 THR cc_start: 0.7541 (p) cc_final: 0.7180 (t) REVERT: J 71 TYR cc_start: 0.8368 (t80) cc_final: 0.7938 (t80) REVERT: J 84 MET cc_start: 0.8447 (tmm) cc_final: 0.7669 (mpp) REVERT: J 171 LEU cc_start: 0.9303 (pp) cc_final: 0.8856 (pp) REVERT: J 326 ASP cc_start: 0.8790 (t0) cc_final: 0.8201 (p0) REVERT: J 476 PRO cc_start: 0.5410 (Cg_endo) cc_final: 0.5189 (Cg_exo) REVERT: J 617 PHE cc_start: 0.8446 (m-80) cc_final: 0.8002 (m-10) REVERT: K 172 LEU cc_start: 0.9084 (pt) cc_final: 0.8208 (tp) REVERT: K 278 MET cc_start: 0.8398 (tpp) cc_final: 0.8042 (tpp) REVERT: K 415 LEU cc_start: 0.5728 (tp) cc_final: 0.5236 (pp) REVERT: K 452 MET cc_start: 0.6206 (mmm) cc_final: 0.5744 (ttt) REVERT: K 637 ASN cc_start: 0.8902 (t0) cc_final: 0.8623 (t0) REVERT: L 149 LEU cc_start: 0.8988 (mt) cc_final: 0.8499 (mt) REVERT: L 161 MET cc_start: 0.8890 (mpp) cc_final: 0.8629 (mpp) REVERT: L 277 ASN cc_start: 0.9217 (m-40) cc_final: 0.8687 (m110) REVERT: L 367 GLU cc_start: 0.6511 (pt0) cc_final: 0.6226 (tt0) REVERT: L 602 ASN cc_start: 0.7963 (p0) cc_final: 0.7547 (p0) REVERT: L 689 TYR cc_start: 0.6062 (p90) cc_final: 0.4969 (p90) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1947 time to fit residues: 116.2808 Evaluate side-chains 292 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 12 optimal weight: 2.9990 chunk 393 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 340 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 974 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27DASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 HIS L 427 GLN ** L 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.082797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.064348 restraints weight = 194121.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065342 restraints weight = 128039.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065396 restraints weight = 87479.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065571 restraints weight = 89414.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065796 restraints weight = 79991.585| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33702 Z= 0.177 Angle : 0.657 10.910 45860 Z= 0.353 Chirality : 0.044 0.231 5075 Planarity : 0.005 0.094 5942 Dihedral : 5.341 31.522 4616 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.41 (0.13), residues: 4214 helix: 0.87 (0.20), residues: 711 sheet: -0.26 (0.15), residues: 1062 loop : -0.58 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 66 TYR 0.027 0.002 TYR A 905 PHE 0.028 0.002 PHE E 29 TRP 0.016 0.002 TRP H 47 HIS 0.005 0.001 HIS J 681 Details of bonding type rmsd covalent geometry : bond 0.00388 (33645) covalent geometry : angle 0.65170 (45746) SS BOND : bond 0.00521 ( 57) SS BOND : angle 1.79797 ( 114) hydrogen bonds : bond 0.04659 ( 1257) hydrogen bonds : angle 5.84352 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5830.54 seconds wall clock time: 102 minutes 0.03 seconds (6120.03 seconds total)