Starting phenix.real_space_refine on Sat Feb 7 22:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4t_39769/02_2026/8z4t_39769.map" } resolution = 3.93 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= -0.001 sd= 0.036 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 186 5.16 5 C 23198 2.51 5 N 6033 2.21 5 O 7016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36433 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7249 Classifications: {'peptide': 941} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 44, 'TRANS': 896} Chain breaks: 5 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 8785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8785 Classifications: {'peptide': 1146} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 2, 'PTRANS': 57, 'TRANS': 1086} Chain breaks: 6 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 8790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8790 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 2, 'PTRANS': 57, 'TRANS': 1084} Chain breaks: 6 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5795 Classifications: {'peptide': 728} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 700} Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 5814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5814 Classifications: {'peptide': 728} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 700} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 7.49, per 1000 atoms: 0.21 Number of scatterers: 36433 At special positions: 0 Unit cell: (170.72, 179.45, 234.74, 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 186 16.00 O 7016 8.00 N 6033 7.00 C 23198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.08 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.02 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.06 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.12 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.09 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.05 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.08 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.06 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.05 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.05 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.05 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.02 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.06 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.12 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.09 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.05 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.08 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.01 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.05 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.05 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.05 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.02 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.06 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.12 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.09 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.05 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 339 " distance=2.05 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 394 " distance=2.06 Simple disulfide: pdb=" SG CYS D 444 " - pdb=" SG CYS D 447 " distance=2.04 Simple disulfide: pdb=" SG CYS D 454 " - pdb=" SG CYS D 472 " distance=2.08 Simple disulfide: pdb=" SG CYS D 649 " - pdb=" SG CYS D 762 " distance=2.04 Simple disulfide: pdb=" SG CYS I 328 " - pdb=" SG CYS I 339 " distance=2.05 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 394 " distance=2.06 Simple disulfide: pdb=" SG CYS I 444 " - pdb=" SG CYS I 447 " distance=2.04 Simple disulfide: pdb=" SG CYS I 454 " - pdb=" SG CYS I 472 " distance=2.08 Simple disulfide: pdb=" SG CYS I 649 " - pdb=" SG CYS I 762 " distance=2.04 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8742 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 80 sheets defined 25.2% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.853A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.150A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.837A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.791A pdb=" N GLN A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.679A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 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 1016 through 1040 removed outlier: 4.172A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.085A 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 1107 removed outlier: 4.319A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.852A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 removed outlier: 4.151A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.641A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 449 through 456 removed outlier: 5.087A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 596 through 600 removed outlier: 3.838A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 628 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN B 842 " --> pdb=" O ALA B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.679A pdb=" N MET B 913 " --> pdb=" O TYR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 940 through 953 Processing helix chain 'B' and resid 954 through 959 Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B1040 " --> pdb=" O LEU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 4.319A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.854A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.151A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.641A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 449 through 456 removed outlier: 5.086A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.838A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 removed outlier: 3.792A pdb=" N GLN C 842 " --> pdb=" O ALA C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.680A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 4.173A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.317A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.540A pdb=" N ASN D 74 " --> pdb=" O LYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.895A pdb=" N PHE D 95 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.623A pdb=" N ILE D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 497 through 506 removed outlier: 3.965A pdb=" N ASN D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 3.506A pdb=" N ASN D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 600 through 616 removed outlier: 3.539A pdb=" N MET D 616 " --> pdb=" O GLN D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 663 through 672 removed outlier: 3.705A pdb=" N TYR D 670 " --> pdb=" O TYR D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 686 removed outlier: 3.583A pdb=" N SER D 686 " --> pdb=" O HIS D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.781A pdb=" N SER D 690 " --> pdb=" O THR D 687 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 726 removed outlier: 4.191A pdb=" N SER D 716 " --> pdb=" O HIS D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 763 Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 71 through 75 removed outlier: 3.540A pdb=" N ASN I 74 " --> pdb=" O LYS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.896A pdb=" N PHE I 95 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 207 Processing helix chain 'I' and resid 290 through 295 removed outlier: 3.623A pdb=" N ILE I 295 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 425 Processing helix chain 'I' and resid 497 through 506 removed outlier: 3.965A pdb=" N ASN I 506 " --> pdb=" O LYS I 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 572 removed outlier: 3.505A pdb=" N ASN I 572 " --> pdb=" O ALA I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 587 through 592 Processing helix chain 'I' and resid 593 through 595 No H-bonds generated for 'chain 'I' and resid 593 through 595' Processing helix chain 'I' and resid 600 through 616 removed outlier: 3.540A pdb=" N MET I 616 " --> pdb=" O GLN I 612 " (cutoff:3.500A) Processing helix chain 'I' and resid 630 through 641 Processing helix chain 'I' and resid 663 through 672 removed outlier: 3.706A pdb=" N TYR I 670 " --> pdb=" O TYR I 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 679 through 686 removed outlier: 3.582A pdb=" N SER I 686 " --> pdb=" O HIS I 682 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 698 removed outlier: 3.781A pdb=" N SER I 690 " --> pdb=" O THR I 687 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU I 693 " --> pdb=" O SER I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 712 through 726 removed outlier: 4.191A pdb=" N SER I 716 " --> pdb=" O HIS I 712 " (cutoff:3.500A) Processing helix chain 'I' and resid 744 through 763 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.599A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.165A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.038A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.167A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.418A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR A 136 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY A 675 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.469A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1191 through 1195 removed outlier: 5.657A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 779 " --> pdb=" O ALA B 969 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.927A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.837A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.073A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AC3, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.166A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.166A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AC7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.418A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.425A pdb=" N THR B 136 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD1, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.572A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 675 " --> pdb=" O PRO B 658 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 373 through 376 removed outlier: 4.760A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.506A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 407 through 408 removed outlier: 7.737A pdb=" N CYS B 407 " --> pdb=" O CYS B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.294A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 724 removed outlier: 6.629A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.468A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1191 through 1195 removed outlier: 5.656A pdb=" N ALA B1193 " --> pdb=" O GLY B1188 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B1188 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.928A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 801 through 804 removed outlier: 4.610A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.071A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE4, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.164A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.039A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.166A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE8, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.417A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 130 removed outlier: 5.426A pdb=" N THR C 136 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF2, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.571A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.507A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 407 through 408 removed outlier: 7.738A pdb=" N CYS C 407 " --> pdb=" O CYS C 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.295A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.631A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.928A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.609A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.073A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 41 through 42 removed outlier: 7.383A pdb=" N LYS D 41 " --> pdb=" O GLN D 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 61 through 62 removed outlier: 5.903A pdb=" N VAL D 78 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 88 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASN D 80 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER D 86 " --> pdb=" O ASN D 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 102 through 107 removed outlier: 9.895A pdb=" N ILE D 102 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN D 119 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR D 120 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR D 129 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 154 through 157 removed outlier: 3.543A pdb=" N TRP D 154 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 194 through 196 Processing sheet with id=AG6, first strand: chain 'D' and resid 194 through 196 removed outlier: 4.220A pdb=" N PHE D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 235 through 240 Processing sheet with id=AG8, first strand: chain 'D' and resid 298 through 307 removed outlier: 5.441A pdb=" N LEU D 300 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 316 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR D 322 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 298 through 307 removed outlier: 5.441A pdb=" N LEU D 300 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 316 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR D 322 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 363 through 364 removed outlier: 4.688A pdb=" N GLN D 388 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP D 393 " --> pdb=" O GLN D 388 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 404 through 410 removed outlier: 5.697A pdb=" N ILE D 407 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE D 418 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS D 441 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 457 through 461 removed outlier: 6.729A pdb=" N LEU D 482 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL D 493 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 511 through 519 removed outlier: 4.641A pdb=" N PHE D 578 " --> pdb=" O ASP D 545 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR D 540 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS D 622 " --> pdb=" O TYR D 540 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU D 542 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE D 624 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 544 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE D 626 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N CYS D 649 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 624 " --> pdb=" O CYS D 649 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE D 651 " --> pdb=" O ILE D 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 626 " --> pdb=" O ILE D 651 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL D 653 " --> pdb=" O ILE D 626 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY D 628 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR D 700 " --> pdb=" O GLN D 731 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET D 733 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 702 " --> pdb=" O MET D 733 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR D 735 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS D 704 " --> pdb=" O TYR D 735 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 41 through 42 removed outlier: 7.383A pdb=" N LYS I 41 " --> pdb=" O GLN I 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'I' and resid 61 through 62 removed outlier: 5.903A pdb=" N VAL I 78 " --> pdb=" O VAL I 88 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 88 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASN I 80 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER I 86 " --> pdb=" O ASN I 80 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 102 through 107 removed outlier: 9.894A pdb=" N ILE I 102 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN I 119 " --> pdb=" O ILE I 102 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR I 120 " --> pdb=" O THR I 129 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR I 129 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 154 through 157 removed outlier: 3.543A pdb=" N TRP I 154 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 194 through 196 Processing sheet with id=AI1, first strand: chain 'I' and resid 194 through 196 removed outlier: 4.219A pdb=" N PHE I 268 " --> pdb=" O ILE I 287 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 235 through 240 Processing sheet with id=AI3, first strand: chain 'I' and resid 298 through 307 removed outlier: 5.442A pdb=" N LEU I 300 " --> pdb=" O LEU I 316 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU I 316 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG I 310 " --> pdb=" O ALA I 306 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR I 322 " --> pdb=" O ARG I 317 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'I' and resid 298 through 307 removed outlier: 5.442A pdb=" N LEU I 300 " --> pdb=" O LEU I 316 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU I 316 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG I 310 " --> pdb=" O ALA I 306 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR I 322 " --> pdb=" O ARG I 317 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'I' and resid 363 through 364 removed outlier: 4.688A pdb=" N GLN I 388 " --> pdb=" O ASP I 393 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP I 393 " --> pdb=" O GLN I 388 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 404 through 410 removed outlier: 5.697A pdb=" N ILE I 407 " --> pdb=" O ILE I 418 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE I 418 " --> pdb=" O ILE I 407 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LYS I 441 " --> pdb=" O GLN I 435 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 457 through 461 removed outlier: 6.729A pdb=" N LEU I 482 " --> pdb=" O VAL I 493 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL I 493 " --> pdb=" O LEU I 482 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I' and resid 511 through 519 removed outlier: 4.640A pdb=" N PHE I 578 " --> pdb=" O ASP I 545 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR I 540 " --> pdb=" O ASP I 620 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS I 622 " --> pdb=" O TYR I 540 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU I 542 " --> pdb=" O LYS I 622 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE I 624 " --> pdb=" O LEU I 542 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU I 544 " --> pdb=" O ILE I 624 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE I 626 " --> pdb=" O LEU I 544 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N CYS I 649 " --> pdb=" O LYS I 622 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE I 624 " --> pdb=" O CYS I 649 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ILE I 651 " --> pdb=" O ILE I 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE I 626 " --> pdb=" O ILE I 651 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL I 653 " --> pdb=" O ILE I 626 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 628 " --> pdb=" O VAL I 653 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR I 700 " --> pdb=" O GLN I 731 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET I 733 " --> pdb=" O TYR I 700 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU I 702 " --> pdb=" O MET I 733 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR I 735 " --> pdb=" O LEU I 702 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS I 704 " --> pdb=" O TYR I 735 " (cutoff:3.500A) 1528 hydrogen bonds defined for protein. 4071 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: 9.18 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.25: 5818 1.25 - 1.40: 10479 1.40 - 1.55: 20584 1.55 - 1.70: 223 1.70 - 1.85: 250 Bond restraints: 37354 Sorted by residual: bond pdb=" C ASN B 870 " pdb=" O ASN B 870 " ideal model delta sigma weight residual 1.235 1.405 -0.170 1.26e-02 6.30e+03 1.82e+02 bond pdb=" C ASN C 870 " pdb=" O ASN C 870 " ideal model delta sigma weight residual 1.235 1.405 -0.170 1.26e-02 6.30e+03 1.81e+02 bond pdb=" C ASN A 870 " pdb=" O ASN A 870 " ideal model delta sigma weight residual 1.235 1.405 -0.170 1.26e-02 6.30e+03 1.81e+02 bond pdb=" C CYS B1106 " pdb=" N VAL B1107 " ideal model delta sigma weight residual 1.329 1.450 -0.121 9.40e-03 1.13e+04 1.65e+02 bond pdb=" C CYS C1106 " pdb=" N VAL C1107 " ideal model delta sigma weight residual 1.329 1.448 -0.119 9.40e-03 1.13e+04 1.60e+02 ... (remaining 37349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 49375 4.10 - 8.19: 1402 8.19 - 12.29: 61 12.29 - 16.38: 13 16.38 - 20.48: 6 Bond angle restraints: 50857 Sorted by residual: angle pdb=" CA CYS B1106 " pdb=" C CYS B1106 " pdb=" O CYS B1106 " ideal model delta sigma weight residual 120.31 134.57 -14.26 1.25e+00 6.40e-01 1.30e+02 angle pdb=" CA CYS A1106 " pdb=" C CYS A1106 " pdb=" O CYS A1106 " ideal model delta sigma weight residual 120.31 134.48 -14.17 1.25e+00 6.40e-01 1.28e+02 angle pdb=" CA CYS C1106 " pdb=" C CYS C1106 " pdb=" O CYS C1106 " ideal model delta sigma weight residual 120.31 134.46 -14.15 1.25e+00 6.40e-01 1.28e+02 angle pdb=" N GLU C 725 " pdb=" CA GLU C 725 " pdb=" C GLU C 725 " ideal model delta sigma weight residual 114.04 102.36 11.68 1.24e+00 6.50e-01 8.88e+01 angle pdb=" N GLU A 725 " pdb=" CA GLU A 725 " pdb=" C GLU A 725 " ideal model delta sigma weight residual 114.04 102.49 11.55 1.24e+00 6.50e-01 8.67e+01 ... (remaining 50852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.35: 20752 18.35 - 36.70: 957 36.70 - 55.05: 246 55.05 - 73.40: 72 73.40 - 91.75: 42 Dihedral angle restraints: 22069 sinusoidal: 8366 harmonic: 13703 Sorted by residual: dihedral pdb=" N CYS B1106 " pdb=" C CYS B1106 " pdb=" CA CYS B1106 " pdb=" CB CYS B1106 " ideal model delta harmonic sigma weight residual 122.80 146.08 -23.28 0 2.50e+00 1.60e-01 8.67e+01 dihedral pdb=" N CYS C1106 " pdb=" C CYS C1106 " pdb=" CA CYS C1106 " pdb=" CB CYS C1106 " ideal model delta harmonic sigma weight residual 122.80 146.06 -23.26 0 2.50e+00 1.60e-01 8.66e+01 dihedral pdb=" N CYS A1106 " pdb=" C CYS A1106 " pdb=" CA CYS A1106 " pdb=" CB CYS A1106 " ideal model delta harmonic sigma weight residual 122.80 146.02 -23.22 0 2.50e+00 1.60e-01 8.63e+01 ... (remaining 22066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 5313 0.225 - 0.450: 225 0.450 - 0.675: 14 0.675 - 0.900: 0 0.900 - 1.125: 6 Chirality restraints: 5558 Sorted by residual: chirality pdb=" CA CYS B1106 " pdb=" N CYS B1106 " pdb=" C CYS B1106 " pdb=" CB CYS B1106 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA CYS C1106 " pdb=" N CYS C1106 " pdb=" C CYS C1106 " pdb=" CB CYS C1106 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CA CYS A1106 " pdb=" N CYS A1106 " pdb=" C CYS A1106 " pdb=" CB CYS A1106 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 5555 not shown) Planarity restraints: 6612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 777 " -0.078 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" CG TYR B 777 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 777 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR B 777 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 777 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR B 777 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR B 777 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 777 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 777 " 0.077 2.00e-02 2.50e+03 4.30e-02 3.70e+01 pdb=" CG TYR C 777 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 777 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR C 777 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 777 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR C 777 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 777 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 777 " 0.077 2.00e-02 2.50e+03 4.29e-02 3.69e+01 pdb=" CG TYR A 777 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 777 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 777 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 777 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A 777 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 777 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 777 " 0.070 2.00e-02 2.50e+03 ... (remaining 6609 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1470 2.68 - 3.23: 34424 3.23 - 3.79: 60121 3.79 - 4.34: 82185 4.34 - 4.90: 131881 Nonbonded interactions: 310081 Sorted by model distance: nonbonded pdb=" NH2 ARG I 596 " pdb=" OD1 ASP I 678 " model vdw 2.121 3.120 nonbonded pdb=" NH2 ARG D 596 " pdb=" OD1 ASP D 678 " model vdw 2.122 3.120 nonbonded pdb=" O ALA D 465 " pdb=" OG SER D 485 " model vdw 2.226 3.040 nonbonded pdb=" O ALA I 465 " pdb=" OG SER I 485 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASP D 329 " pdb=" NH1 ARG D 343 " model vdw 2.254 3.120 ... (remaining 310076 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 'B' and (resid 19 through 374 or resid 382 through 579 or (resid 580 and \ (name N or name CA or name C or name O or name CB )) or resid 581 through 594 or \ (resid 595 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 6 through 1224)) selection = (chain 'C' and (resid 19 through 387 or (resid 388 and (name N or name CA or nam \ e C or name O or name CB )) or resid 389 through 402 or (resid 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 through 411 or (resid 4 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 413 through \ 415 or (resid 416 and (name N or name CA or name C or name O or name CB )) or r \ esid 417 through 434 or (resid 435 and (name N or name CA or name C or name O or \ name CB )) or resid 436 through 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB )) or resid 440 through 453 or (resid 454 and (name N o \ r name CA or name C or name O or name CB )) or resid 455 through 457 or (resid 4 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 459 through \ 476 or (resid 477 and (name N or name CA or name C or name O or name CB )) or r \ esid 478 through 482 or (resid 483 through 484 and (name N or name CA or name C \ or name O or name CB )) or resid 485 through 488 or (resid 489 and (name N or na \ me CA or name C or name O or name CB )) or resid 490 through 500 or (resid 501 a \ nd (name N or name CA or name C or name O or name CB )) or resid 502 through 509 \ or (resid 510 and (name N or name CA or name C or name O or name CB )) or resid \ 511 through 531 or (resid 532 and (name N or name CA or name C or name O or nam \ e CB )) or resid 533 through 1224)) } ncs_group { reference = chain 'D' selection = (chain 'I' and (resid 39 through 536 or (resid 537 through 538 and (name N or na \ me CA or name C or name O or name CB )) or resid 539 through 562 or (resid 563 t \ hrough 564 and (name N or name CA or name C or name O or name CB )) or resid 565 \ through 572 or (resid 573 and (name N or name CA or name C or name O or name CB \ )) or resid 574 through 623 or (resid 624 through 625 and (name N or name CA or \ name C or name O or name CB )) or resid 626 through 672 or (resid 673 and (name \ N or name CA or name C or name O or name CB )) or resid 674 through 766)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.460 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1123 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 : 0.020 0.186 37411 Z= 1.085 Angle : 1.756 45.931 50971 Z= 1.148 Chirality : 0.116 1.125 5558 Planarity : 0.008 0.051 6612 Dihedral : 12.603 91.751 13156 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.90 % Favored : 95.76 % Rotamer: Outliers : 0.61 % Allowed : 5.18 % Favored : 94.21 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.96 % 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: -0.90 (0.11), residues: 4643 helix: -1.12 (0.14), residues: 932 sheet: -0.30 (0.13), residues: 1221 loop : -0.41 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 190 TYR 0.080 0.008 TYR C 184 PHE 0.040 0.005 PHE C 323 TRP 0.028 0.005 TRP I 201 HIS 0.010 0.002 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.01985 (37354) covalent geometry : angle 1.66530 (50857) SS BOND : bond 0.03297 ( 57) SS BOND : angle 11.89995 ( 114) hydrogen bonds : bond 0.13975 ( 1500) hydrogen bonds : angle 8.06054 ( 4071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 524 time to evaluate : 1.023 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: C 416 SER cc_start: 0.4487 (OUTLIER) cc_final: 0.3757 (p) REVERT: C 510 ASP cc_start: -0.0634 (OUTLIER) cc_final: -0.1422 (p0) REVERT: C 625 VAL cc_start: 0.3984 (t) cc_final: 0.3225 (p) REVERT: C 939 MET cc_start: -0.0342 (mtt) cc_final: -0.0726 (mtm) REVERT: C 943 MET cc_start: 0.4142 (ttm) cc_final: 0.3835 (tpt) REVERT: C 1076 THR cc_start: 0.7262 (m) cc_final: 0.6963 (m) REVERT: C 1135 TYR cc_start: 0.2063 (t80) cc_final: 0.1591 (t80) REVERT: C 1171 TYR cc_start: 0.2590 (m-80) cc_final: 0.1746 (m-10) REVERT: I 187 TRP cc_start: -0.1001 (m-90) cc_final: -0.1899 (p90) REVERT: I 357 PHE cc_start: 0.1409 (m-80) cc_final: 0.0776 (m-80) outliers start: 24 outliers final: 7 residues processed: 548 average time/residue: 0.2119 time to fit residues: 189.5824 Evaluate side-chains 328 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 319 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 624 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 107 GLN A 280 GLN A 319 GLN A 599 GLN A 708 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 993 ASN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1129 ASN A1145 ASN ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN B 81 HIS B 475 ASN B 619 ASN B 766 HIS B 812 ASN B 815 GLN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 ASN B1016 ASN B1023 GLN B1027 ASN B1042 ASN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 319 GLN C 421 ASN C 602 ASN C 733 GLN C 815 GLN C 836 HIS C 993 ASN C1072 ASN C1104 ASN C1129 ASN C1145 ASN D 66 HIS ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 196 ASN D 227 GLN D 314 GLN D 527 GLN I 66 HIS I 196 ASN I 227 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5411 r_free = 0.5411 target = 0.261862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5290 r_free = 0.5290 target = 0.250076 restraints weight = 139481.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.250611 restraints weight = 145106.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.251707 restraints weight = 97523.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.251383 restraints weight = 66951.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.251675 restraints weight = 70641.611| |-----------------------------------------------------------------------------| r_work (final): 0.5305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3032 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.134 37411 Z= 0.390 Angle : 1.053 20.610 50971 Z= 0.575 Chirality : 0.060 0.382 5558 Planarity : 0.008 0.115 6612 Dihedral : 6.847 57.528 5126 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.83 % Allowed : 9.80 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.16 (0.11), residues: 4643 helix: -0.99 (0.15), residues: 927 sheet: -0.35 (0.14), residues: 1220 loop : -0.81 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG A 269 TYR 0.066 0.004 TYR C 932 PHE 0.064 0.004 PHE C1126 TRP 0.035 0.003 TRP B 253 HIS 0.018 0.003 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00842 (37354) covalent geometry : angle 1.04258 (50857) SS BOND : bond 0.01385 ( 57) SS BOND : angle 3.25595 ( 114) hydrogen bonds : bond 0.06770 ( 1500) hydrogen bonds : angle 7.73757 ( 4071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 411 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 TYR cc_start: 0.2506 (m-80) cc_final: 0.2205 (p90) REVERT: A 632 TYR cc_start: 0.5413 (m-80) cc_final: 0.5115 (m-80) REVERT: A 913 MET cc_start: 0.6303 (tpp) cc_final: 0.5961 (tpt) REVERT: A 928 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.4821 (m-80) REVERT: A 967 PHE cc_start: 0.1185 (t80) cc_final: 0.0295 (t80) REVERT: B 109 VAL cc_start: 0.6610 (t) cc_final: 0.6352 (p) REVERT: B 206 THR cc_start: 0.5393 (p) cc_final: 0.5171 (p) REVERT: B 651 LEU cc_start: 0.7733 (tp) cc_final: 0.7515 (mp) REVERT: B 852 SER cc_start: 0.5422 (OUTLIER) cc_final: 0.4527 (m) REVERT: B 906 MET cc_start: 0.5784 (pmm) cc_final: 0.5461 (pmm) REVERT: B 1137 MET cc_start: 0.1795 (OUTLIER) cc_final: 0.0738 (mmm) REVERT: C 24 ASP cc_start: 0.3955 (OUTLIER) cc_final: 0.2497 (t0) REVERT: C 71 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5451 (t80) REVERT: C 75 PHE cc_start: 0.7521 (m-80) cc_final: 0.6807 (m-80) REVERT: C 77 TYR cc_start: 0.6293 (m-80) cc_final: 0.5960 (m-80) REVERT: C 415 LEU cc_start: -0.1700 (OUTLIER) cc_final: -0.1939 (tt) REVERT: C 416 SER cc_start: 0.5044 (OUTLIER) cc_final: 0.3882 (t) REVERT: C 495 LEU cc_start: 0.2434 (OUTLIER) cc_final: 0.1894 (tt) REVERT: C 510 ASP cc_start: -0.1212 (OUTLIER) cc_final: -0.1909 (p0) REVERT: C 625 VAL cc_start: 0.6068 (t) cc_final: 0.5773 (t) REVERT: C 770 VAL cc_start: 0.3885 (OUTLIER) cc_final: 0.3671 (p) REVERT: C 863 PRO cc_start: 0.3848 (Cg_exo) cc_final: 0.3543 (Cg_endo) REVERT: C 939 MET cc_start: 0.0170 (mtt) cc_final: -0.1086 (ttm) REVERT: C 1136 PHE cc_start: 0.4056 (OUTLIER) cc_final: 0.3602 (t80) REVERT: D 68 TYR cc_start: 0.2985 (p90) cc_final: 0.2640 (p90) REVERT: D 115 LEU cc_start: 0.3398 (tt) cc_final: 0.3072 (tt) REVERT: D 201 TRP cc_start: -0.1329 (t60) cc_final: -0.1821 (t60) REVERT: D 322 TYR cc_start: 0.1503 (t80) cc_final: -0.0211 (m-80) REVERT: D 325 MET cc_start: 0.3195 (ptm) cc_final: 0.2845 (ptm) REVERT: D 660 GLU cc_start: 0.2704 (OUTLIER) cc_final: 0.1992 (tp30) REVERT: I 357 PHE cc_start: 0.1696 (m-80) cc_final: 0.1106 (m-80) REVERT: I 595 ASN cc_start: -0.0549 (t0) cc_final: -0.0868 (m-40) outliers start: 111 outliers final: 54 residues processed: 498 average time/residue: 0.2077 time to fit residues: 171.7603 Evaluate side-chains 387 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1026 VAL Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 828 CYS Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 855 SER Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1190 SER Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 71 TYR Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 806 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 898 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain C residue 1141 TYR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 573 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 77 optimal weight: 0.5980 chunk 385 optimal weight: 40.0000 chunk 89 optimal weight: 2.9990 chunk 364 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 424 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 142 optimal weight: 50.0000 chunk 300 optimal weight: 1.9990 chunk 393 optimal weight: 50.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 619 ASN A 800 GLN ** A1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN B1023 GLN B1027 ASN B1042 ASN ** B1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 ASN C1110 GLN D 314 GLN D 553 GLN ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5411 r_free = 0.5411 target = 0.261349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.250352 restraints weight = 139528.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.250246 restraints weight = 172416.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.251474 restraints weight = 127508.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5293 r_free = 0.5293 target = 0.251252 restraints weight = 89152.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.251551 restraints weight = 84096.785| |-----------------------------------------------------------------------------| r_work (final): 0.5306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3028 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37411 Z= 0.188 Angle : 0.704 15.398 50971 Z= 0.380 Chirality : 0.048 0.447 5558 Planarity : 0.005 0.071 6612 Dihedral : 5.734 52.604 5121 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.88 % Allowed : 11.92 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4643 helix: -0.30 (0.16), residues: 927 sheet: -0.24 (0.14), residues: 1236 loop : -0.70 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1113 TYR 0.042 0.002 TYR A 77 PHE 0.027 0.002 PHE C 147 TRP 0.019 0.002 TRP C 960 HIS 0.010 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00411 (37354) covalent geometry : angle 0.69687 (50857) SS BOND : bond 0.00699 ( 57) SS BOND : angle 2.21317 ( 114) hydrogen bonds : bond 0.04749 ( 1500) hydrogen bonds : angle 6.86795 ( 4071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 370 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5677 (tm-30) REVERT: A 240 MET cc_start: 0.5252 (mmm) cc_final: 0.4850 (mmt) REVERT: A 757 MET cc_start: 0.0498 (mpp) cc_final: 0.0295 (mpp) REVERT: A 913 MET cc_start: 0.6214 (tpp) cc_final: 0.5955 (tpt) REVERT: A 928 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: A 967 PHE cc_start: 0.0644 (t80) cc_final: -0.0731 (t80) REVERT: B 69 ILE cc_start: 0.6298 (pt) cc_final: 0.6066 (pt) REVERT: B 83 ASP cc_start: 0.4273 (p0) cc_final: 0.3620 (p0) REVERT: B 109 VAL cc_start: 0.6619 (t) cc_final: 0.6239 (p) REVERT: B 651 LEU cc_start: 0.7862 (tp) cc_final: 0.7660 (mp) REVERT: B 939 MET cc_start: 0.7122 (mmm) cc_final: 0.6725 (mmt) REVERT: C 24 ASP cc_start: 0.3485 (OUTLIER) cc_final: 0.2127 (t0) REVERT: C 60 GLN cc_start: 0.6144 (tp40) cc_final: 0.5799 (tp40) REVERT: C 75 PHE cc_start: 0.7674 (m-80) cc_final: 0.6944 (m-80) REVERT: C 77 TYR cc_start: 0.6216 (m-80) cc_final: 0.5736 (m-10) REVERT: C 401 ARG cc_start: -0.1724 (OUTLIER) cc_final: -0.3721 (mtp180) REVERT: C 495 LEU cc_start: 0.2108 (OUTLIER) cc_final: 0.1875 (tt) REVERT: C 510 ASP cc_start: -0.1321 (OUTLIER) cc_final: -0.2109 (p0) REVERT: C 939 MET cc_start: 0.0151 (mtt) cc_final: -0.0954 (ttm) REVERT: C 1076 THR cc_start: 0.7923 (m) cc_final: 0.7701 (t) REVERT: C 1084 GLN cc_start: 0.6333 (tt0) cc_final: 0.6114 (tt0) REVERT: C 1129 ASN cc_start: 0.1816 (OUTLIER) cc_final: 0.0839 (t0) REVERT: C 1136 PHE cc_start: 0.3588 (OUTLIER) cc_final: 0.3352 (t80) REVERT: D 68 TYR cc_start: 0.2824 (p90) cc_final: 0.2546 (p90) REVERT: D 187 TRP cc_start: 0.0239 (p-90) cc_final: -0.1195 (p90) REVERT: D 201 TRP cc_start: -0.1217 (t60) cc_final: -0.1637 (t60) REVERT: D 322 TYR cc_start: 0.1133 (t80) cc_final: 0.0069 (m-80) REVERT: D 553 GLN cc_start: -0.0252 (OUTLIER) cc_final: -0.0894 (tp40) REVERT: I 357 PHE cc_start: 0.1603 (m-80) cc_final: 0.1049 (m-80) REVERT: I 420 ASN cc_start: 0.4924 (p0) cc_final: 0.4717 (p0) outliers start: 113 outliers final: 54 residues processed: 449 average time/residue: 0.2082 time to fit residues: 155.4074 Evaluate side-chains 377 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 314 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1042 ASN Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 24 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 806 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 898 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1129 ASN Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 630 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 228 optimal weight: 30.0000 chunk 413 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 407 optimal weight: 40.0000 chunk 119 optimal weight: 0.1980 chunk 324 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 765 ASN A 772 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 833 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1020 GLN ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN D 74 ASN D 314 GLN D 369 ASN ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 592 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5377 r_free = 0.5377 target = 0.257701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.245283 restraints weight = 136366.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.245495 restraints weight = 158406.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.246125 restraints weight = 120370.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.246064 restraints weight = 83168.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.246432 restraints weight = 74059.776| |-----------------------------------------------------------------------------| r_work (final): 0.5254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3309 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 37411 Z= 0.216 Angle : 0.720 14.541 50971 Z= 0.388 Chirality : 0.048 0.290 5558 Planarity : 0.005 0.077 6612 Dihedral : 5.757 54.948 5120 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.22 % Allowed : 13.07 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.99 (0.12), residues: 4643 helix: -0.39 (0.16), residues: 907 sheet: -0.42 (0.14), residues: 1223 loop : -0.80 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 62 TYR 0.045 0.002 TYR B 947 PHE 0.031 0.002 PHE C1126 TRP 0.028 0.002 TRP B 253 HIS 0.013 0.002 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00469 (37354) covalent geometry : angle 0.71206 (50857) SS BOND : bond 0.00767 ( 57) SS BOND : angle 2.34349 ( 114) hydrogen bonds : bond 0.04754 ( 1500) hydrogen bonds : angle 7.03626 ( 4071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 353 time to evaluate : 1.086 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: A 72 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: A 316 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4729 (m-80) REVERT: A 913 MET cc_start: 0.6279 (tpp) cc_final: 0.6066 (tpt) REVERT: A 928 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.4568 (m-80) REVERT: A 1008 MET cc_start: 0.4991 (mmt) cc_final: 0.4443 (mmt) REVERT: B 48 ILE cc_start: 0.2945 (OUTLIER) cc_final: 0.2743 (mm) REVERT: B 806 CYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5578 (t) REVERT: B 939 MET cc_start: 0.7026 (mmm) cc_final: 0.6693 (mmt) REVERT: B 1142 TYR cc_start: 0.3072 (OUTLIER) cc_final: 0.2811 (m-80) REVERT: C 75 PHE cc_start: 0.7938 (m-80) cc_final: 0.6971 (m-80) REVERT: C 401 ARG cc_start: -0.1688 (OUTLIER) cc_final: -0.3662 (mtp180) REVERT: C 510 ASP cc_start: -0.1552 (OUTLIER) cc_final: -0.2619 (p0) REVERT: C 939 MET cc_start: 0.0345 (mtt) cc_final: -0.0465 (ttm) REVERT: C 943 MET cc_start: 0.5844 (ttt) cc_final: 0.5455 (tpp) REVERT: C 951 LEU cc_start: 0.0721 (OUTLIER) cc_final: -0.1457 (tp) REVERT: C 1075 LEU cc_start: 0.6750 (mm) cc_final: 0.6542 (mm) REVERT: C 1129 ASN cc_start: 0.2123 (OUTLIER) cc_final: 0.1416 (t0) REVERT: C 1136 PHE cc_start: 0.3622 (OUTLIER) cc_final: 0.3069 (t80) REVERT: D 68 TYR cc_start: 0.2938 (p90) cc_final: 0.2621 (p90) REVERT: D 115 LEU cc_start: 0.3925 (tt) cc_final: 0.3664 (tt) REVERT: D 187 TRP cc_start: 0.0086 (p-90) cc_final: -0.0687 (p-90) REVERT: D 201 TRP cc_start: -0.1365 (t60) cc_final: -0.1749 (t60) REVERT: D 322 TYR cc_start: 0.1134 (t80) cc_final: -0.0029 (m-80) REVERT: I 196 ASN cc_start: -0.0674 (m-40) cc_final: -0.1288 (m110) REVERT: I 219 ASN cc_start: 0.3079 (m110) cc_final: 0.2840 (m110) REVERT: I 651 ILE cc_start: 0.1203 (OUTLIER) cc_final: 0.0705 (tt) REVERT: I 715 GLN cc_start: -0.3308 (OUTLIER) cc_final: -0.3522 (mt0) outliers start: 126 outliers final: 80 residues processed: 452 average time/residue: 0.1954 time to fit residues: 150.3801 Evaluate side-chains 393 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 300 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 253 TRP Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 803 THR Chi-restraints excluded: chain B residue 806 CYS Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 147 PHE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 603 CYS Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 898 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1129 ASN Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 630 SER Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 87 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 455 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 316 optimal weight: 20.0000 chunk 254 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 420 optimal weight: 40.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN A1132 ASN ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN C1213 ASN D 314 GLN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5378 r_free = 0.5378 target = 0.257730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.246486 restraints weight = 135452.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.246497 restraints weight = 162782.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.246185 restraints weight = 116103.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.246034 restraints weight = 102704.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.246423 restraints weight = 81811.066| |-----------------------------------------------------------------------------| r_work (final): 0.5261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3299 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37411 Z= 0.161 Angle : 0.650 12.338 50971 Z= 0.345 Chirality : 0.046 0.247 5558 Planarity : 0.005 0.066 6612 Dihedral : 5.388 53.129 5120 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 14.19 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 4643 helix: -0.18 (0.16), residues: 914 sheet: -0.48 (0.14), residues: 1204 loop : -0.70 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 847 TYR 0.037 0.002 TYR B 947 PHE 0.025 0.002 PHE C 147 TRP 0.018 0.001 TRP B 253 HIS 0.011 0.001 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00349 (37354) covalent geometry : angle 0.64402 (50857) SS BOND : bond 0.00781 ( 57) SS BOND : angle 1.97596 ( 114) hydrogen bonds : bond 0.04215 ( 1500) hydrogen bonds : angle 6.71791 ( 4071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 329 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6289 (tm-30) REVERT: A 179 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.4693 (pp) REVERT: A 1137 MET cc_start: 0.5048 (mmm) cc_final: 0.4813 (mmm) REVERT: B 935 LEU cc_start: 0.6510 (mm) cc_final: 0.6180 (mp) REVERT: C 75 PHE cc_start: 0.7803 (m-80) cc_final: 0.6926 (m-80) REVERT: C 252 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.3338 (tt0) REVERT: C 401 ARG cc_start: -0.1483 (OUTLIER) cc_final: -0.3637 (mtp180) REVERT: C 939 MET cc_start: 0.0297 (mtt) cc_final: -0.0718 (ptm) REVERT: C 951 LEU cc_start: 0.0666 (OUTLIER) cc_final: -0.1551 (tp) REVERT: C 1082 VAL cc_start: 0.7032 (m) cc_final: 0.6663 (p) REVERT: C 1136 PHE cc_start: 0.3355 (OUTLIER) cc_final: 0.2896 (t80) REVERT: D 68 TYR cc_start: 0.2950 (p90) cc_final: 0.2515 (p90) REVERT: D 115 LEU cc_start: 0.3904 (tt) cc_final: 0.3272 (tt) REVERT: D 157 TRP cc_start: 0.2225 (m100) cc_final: 0.2005 (m100) REVERT: D 187 TRP cc_start: 0.0175 (p-90) cc_final: -0.1425 (p90) REVERT: D 201 TRP cc_start: -0.1404 (t60) cc_final: -0.1740 (t60) REVERT: D 322 TYR cc_start: 0.1155 (t80) cc_final: 0.0145 (m-80) REVERT: D 325 MET cc_start: 0.3231 (OUTLIER) cc_final: 0.0665 (mtm) REVERT: D 358 ARG cc_start: 0.4206 (ptt180) cc_final: 0.3063 (ttm110) REVERT: D 761 GLN cc_start: 0.4000 (tm-30) cc_final: 0.3483 (mt0) REVERT: I 196 ASN cc_start: -0.0646 (m-40) cc_final: -0.1027 (m-40) REVERT: I 219 ASN cc_start: 0.3451 (m110) cc_final: 0.3147 (m-40) REVERT: I 357 PHE cc_start: 0.1510 (m-80) cc_final: 0.0939 (m-80) REVERT: I 651 ILE cc_start: 0.1801 (OUTLIER) cc_final: 0.1276 (tt) REVERT: I 715 GLN cc_start: -0.3229 (OUTLIER) cc_final: -0.3430 (mt0) outliers start: 119 outliers final: 73 residues processed: 416 average time/residue: 0.1997 time to fit residues: 140.8763 Evaluate side-chains 387 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 305 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 228 PHE Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 898 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 715 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 308 optimal weight: 0.9990 chunk 355 optimal weight: 50.0000 chunk 16 optimal weight: 0.7980 chunk 370 optimal weight: 50.0000 chunk 448 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 406 optimal weight: 50.0000 chunk 187 optimal weight: 5.9990 chunk 422 optimal weight: 50.0000 chunk 120 optimal weight: 0.0870 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 208 HIS ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS D 553 GLN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5347 r_free = 0.5347 target = 0.254344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.242194 restraints weight = 135105.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5196 r_free = 0.5196 target = 0.241991 restraints weight = 179518.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.242710 restraints weight = 155884.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.242653 restraints weight = 105152.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.242937 restraints weight = 97543.634| |-----------------------------------------------------------------------------| r_work (final): 0.5219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3482 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 37411 Z= 0.216 Angle : 0.736 14.694 50971 Z= 0.393 Chirality : 0.049 0.304 5558 Planarity : 0.005 0.083 6612 Dihedral : 5.686 53.597 5118 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 3.62 % Allowed : 14.80 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.13 (0.12), residues: 4643 helix: -0.39 (0.16), residues: 909 sheet: -0.61 (0.15), residues: 1201 loop : -0.88 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1069 TYR 0.044 0.002 TYR B 947 PHE 0.046 0.002 PHE B 279 TRP 0.017 0.001 TRP C 960 HIS 0.012 0.002 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00467 (37354) covalent geometry : angle 0.73191 (50857) SS BOND : bond 0.01476 ( 57) SS BOND : angle 1.78415 ( 114) hydrogen bonds : bond 0.04664 ( 1500) hydrogen bonds : angle 7.08088 ( 4071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 326 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: A 352 GLU cc_start: 0.5005 (tp30) cc_final: 0.4799 (tp30) REVERT: A 822 ARG cc_start: 0.6362 (mtm-85) cc_final: 0.6019 (mmm160) REVERT: A 955 ILE cc_start: 0.2041 (OUTLIER) cc_final: 0.1469 (pt) REVERT: A 1008 MET cc_start: 0.5013 (mmt) cc_final: 0.4476 (mmt) REVERT: A 1069 ARG cc_start: 0.6754 (ttp-170) cc_final: 0.6485 (ttp-170) REVERT: B 674 PHE cc_start: 0.3973 (m-80) cc_final: 0.3726 (m-10) REVERT: B 1142 TYR cc_start: 0.4122 (OUTLIER) cc_final: 0.3462 (m-80) REVERT: C 67 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6598 (mm) REVERT: C 281 PHE cc_start: 0.6461 (t80) cc_final: 0.6040 (t80) REVERT: C 401 ARG cc_start: -0.1495 (OUTLIER) cc_final: -0.3434 (mtp180) REVERT: C 757 MET cc_start: 0.3562 (pmm) cc_final: 0.3008 (mpp) REVERT: C 799 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5733 (pt) REVERT: C 951 LEU cc_start: 0.1155 (OUTLIER) cc_final: -0.2749 (mp) REVERT: C 979 ARG cc_start: 0.1807 (OUTLIER) cc_final: -0.0102 (mtt90) REVERT: C 1082 VAL cc_start: 0.6862 (m) cc_final: 0.6650 (t) REVERT: D 68 TYR cc_start: 0.3116 (p90) cc_final: 0.2818 (p90) REVERT: D 187 TRP cc_start: 0.0160 (p-90) cc_final: -0.1257 (p90) REVERT: D 322 TYR cc_start: 0.1267 (t80) cc_final: 0.0245 (m-80) REVERT: D 358 ARG cc_start: 0.4147 (ptt180) cc_final: 0.3020 (ttm110) REVERT: D 660 GLU cc_start: 0.2504 (OUTLIER) cc_final: 0.1608 (tp30) REVERT: D 761 GLN cc_start: 0.3879 (tm-30) cc_final: 0.3439 (mt0) REVERT: I 196 ASN cc_start: -0.0434 (m-40) cc_final: -0.0828 (m-40) REVERT: I 219 ASN cc_start: 0.3628 (m110) cc_final: 0.3399 (m-40) REVERT: I 357 PHE cc_start: 0.1435 (m-80) cc_final: 0.0845 (m-80) REVERT: I 573 ILE cc_start: 0.3143 (OUTLIER) cc_final: 0.2803 (tp) REVERT: I 651 ILE cc_start: 0.1898 (OUTLIER) cc_final: 0.1371 (tt) REVERT: I 715 GLN cc_start: -0.2996 (OUTLIER) cc_final: -0.3237 (mt0) outliers start: 142 outliers final: 93 residues processed: 433 average time/residue: 0.1928 time to fit residues: 141.0956 Evaluate side-chains 389 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 284 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 332 TYR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 947 TYR Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1042 ASN Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 898 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 979 ARG Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain D residue 660 GLU Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 265 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 630 SER Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 387 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 337 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 30.0000 chunk 66 optimal weight: 0.0000 chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN B 406 ASN B 475 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN C1110 GLN C1122 HIS D 679 ASN ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.253561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.240893 restraints weight = 133786.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5190 r_free = 0.5190 target = 0.241420 restraints weight = 164380.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.240505 restraints weight = 119206.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.240313 restraints weight = 105913.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.240508 restraints weight = 95934.483| |-----------------------------------------------------------------------------| r_work (final): 0.5197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3588 moved from start: 0.8345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37411 Z= 0.186 Angle : 0.689 20.654 50971 Z= 0.367 Chirality : 0.047 0.237 5558 Planarity : 0.005 0.083 6612 Dihedral : 5.515 51.713 5118 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 3.32 % Allowed : 15.98 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.12 (0.12), residues: 4643 helix: -0.33 (0.16), residues: 916 sheet: -0.60 (0.15), residues: 1174 loop : -0.90 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1069 TYR 0.036 0.002 TYR B 947 PHE 0.031 0.002 PHE D 713 TRP 0.019 0.001 TRP A 960 HIS 0.037 0.002 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00408 (37354) covalent geometry : angle 0.68535 (50857) SS BOND : bond 0.00980 ( 57) SS BOND : angle 1.72881 ( 114) hydrogen bonds : bond 0.04413 ( 1500) hydrogen bonds : angle 6.92001 ( 4071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 318 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6668 (OUTLIER) cc_final: 0.6328 (tm-30) REVERT: A 757 MET cc_start: 0.0440 (mpp) cc_final: 0.0231 (mpp) REVERT: A 932 TYR cc_start: 0.5529 (p90) cc_final: 0.5327 (p90) REVERT: A 1008 MET cc_start: 0.5102 (mmt) cc_final: 0.4635 (mmt) REVERT: A 1171 TYR cc_start: 0.0141 (OUTLIER) cc_final: -0.2471 (m-80) REVERT: B 1142 TYR cc_start: 0.4275 (OUTLIER) cc_final: 0.1928 (t80) REVERT: C 67 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6568 (mm) REVERT: C 401 ARG cc_start: -0.1231 (OUTLIER) cc_final: -0.3246 (mtp180) REVERT: C 415 LEU cc_start: -0.1299 (OUTLIER) cc_final: -0.1765 (tp) REVERT: C 626 ARG cc_start: 0.1867 (OUTLIER) cc_final: -0.0107 (mmm160) REVERT: C 770 VAL cc_start: 0.4477 (OUTLIER) cc_final: 0.4011 (m) REVERT: C 928 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: C 951 LEU cc_start: 0.0888 (OUTLIER) cc_final: -0.2701 (mt) REVERT: D 68 TYR cc_start: 0.3024 (p90) cc_final: 0.2653 (p90) REVERT: D 132 TYR cc_start: 0.4101 (m-80) cc_final: 0.3648 (m-80) REVERT: D 322 TYR cc_start: 0.1357 (t80) cc_final: 0.0370 (m-80) REVERT: D 671 MET cc_start: -0.0299 (OUTLIER) cc_final: -0.0947 (tpt) REVERT: D 761 GLN cc_start: 0.3847 (tm-30) cc_final: 0.3404 (mt0) REVERT: I 196 ASN cc_start: -0.0323 (m-40) cc_final: -0.0794 (m110) REVERT: I 219 ASN cc_start: 0.3712 (m110) cc_final: 0.3467 (m-40) REVERT: I 229 ASN cc_start: 0.0901 (t0) cc_final: 0.0670 (t0) REVERT: I 357 PHE cc_start: 0.1456 (m-80) cc_final: 0.0881 (m-80) REVERT: I 573 ILE cc_start: 0.2840 (OUTLIER) cc_final: 0.2506 (tp) REVERT: I 651 ILE cc_start: 0.1729 (OUTLIER) cc_final: 0.1243 (tt) REVERT: I 715 GLN cc_start: -0.3152 (OUTLIER) cc_final: -0.3352 (mt0) outliers start: 130 outliers final: 91 residues processed: 419 average time/residue: 0.1988 time to fit residues: 139.2023 Evaluate side-chains 389 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 284 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1171 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 827 PHE Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 ASN Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 671 MET Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 443 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 290 optimal weight: 0.0030 chunk 64 optimal weight: 0.7980 chunk 428 optimal weight: 9.9990 chunk 437 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 overall best weight: 4.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1213 ASN B 618 GLN B 681 HIS ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 ASN B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 155 ASN ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5307 r_free = 0.5307 target = 0.249923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.234726 restraints weight = 131937.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.234579 restraints weight = 157934.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.235273 restraints weight = 123679.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.235081 restraints weight = 83749.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.235376 restraints weight = 80225.461| |-----------------------------------------------------------------------------| r_work (final): 0.5137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3826 moved from start: 0.9349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 37411 Z= 0.255 Angle : 0.807 23.206 50971 Z= 0.433 Chirality : 0.051 0.276 5558 Planarity : 0.006 0.079 6612 Dihedral : 6.061 50.962 5118 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.57 % Allowed : 16.33 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.41 (0.12), residues: 4643 helix: -0.65 (0.16), residues: 897 sheet: -0.64 (0.15), residues: 1139 loop : -1.14 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 921 TYR 0.048 0.003 TYR B 947 PHE 0.051 0.003 PHE A1001 TRP 0.030 0.002 TRP D 187 HIS 0.020 0.002 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00566 (37354) covalent geometry : angle 0.80275 (50857) SS BOND : bond 0.00693 ( 57) SS BOND : angle 1.87946 ( 114) hydrogen bonds : bond 0.05240 ( 1500) hydrogen bonds : angle 7.40976 ( 4071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 318 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: A 149 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5725 (mm) REVERT: A 240 MET cc_start: 0.5186 (mmm) cc_final: 0.3421 (mmm) REVERT: A 757 MET cc_start: 0.1146 (mpp) cc_final: 0.0541 (mpp) REVERT: A 858 SER cc_start: 0.5572 (t) cc_final: 0.4963 (t) REVERT: A 955 ILE cc_start: 0.2115 (OUTLIER) cc_final: 0.1339 (pt) REVERT: A 1171 TYR cc_start: 0.0141 (OUTLIER) cc_final: -0.2570 (m-80) REVERT: B 347 LEU cc_start: 0.7326 (tp) cc_final: 0.6955 (tt) REVERT: B 857 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4460 (mt0) REVERT: B 1142 TYR cc_start: 0.4923 (OUTLIER) cc_final: 0.2412 (t80) REVERT: C 269 ARG cc_start: 0.6813 (tpt90) cc_final: 0.5344 (tpp-160) REVERT: C 401 ARG cc_start: -0.1164 (OUTLIER) cc_final: -0.3189 (mtp180) REVERT: C 415 LEU cc_start: -0.1082 (OUTLIER) cc_final: -0.1624 (tp) REVERT: C 626 ARG cc_start: 0.2609 (OUTLIER) cc_final: 0.0883 (mmm160) REVERT: C 786 PHE cc_start: 0.3491 (OUTLIER) cc_final: 0.2091 (p90) REVERT: C 799 ILE cc_start: 0.6405 (OUTLIER) cc_final: 0.5793 (pt) REVERT: C 928 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: C 943 MET cc_start: 0.5358 (tpp) cc_final: 0.4820 (tpt) REVERT: C 951 LEU cc_start: 0.0803 (OUTLIER) cc_final: -0.3410 (mt) REVERT: C 965 SER cc_start: 0.7789 (m) cc_final: 0.6985 (t) REVERT: C 1033 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7170 (tp) REVERT: D 68 TYR cc_start: 0.3303 (p90) cc_final: 0.2854 (p90) REVERT: D 132 TYR cc_start: 0.4001 (m-80) cc_final: 0.3612 (m-80) REVERT: D 187 TRP cc_start: 0.0936 (p-90) cc_final: -0.1688 (p90) REVERT: D 322 TYR cc_start: 0.1680 (t80) cc_final: 0.0356 (m-80) REVERT: D 671 MET cc_start: 0.0429 (OUTLIER) cc_final: -0.0129 (tpp) REVERT: D 761 GLN cc_start: 0.3782 (OUTLIER) cc_final: 0.3256 (mt0) REVERT: I 186 THR cc_start: 0.0834 (OUTLIER) cc_final: -0.0476 (m) REVERT: I 573 ILE cc_start: 0.2824 (OUTLIER) cc_final: 0.2523 (tp) REVERT: I 651 ILE cc_start: 0.1822 (OUTLIER) cc_final: 0.1291 (tt) REVERT: I 715 GLN cc_start: -0.2627 (OUTLIER) cc_final: -0.2859 (mt0) outliers start: 140 outliers final: 94 residues processed: 426 average time/residue: 0.2170 time to fit residues: 152.8954 Evaluate side-chains 391 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 277 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 316 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1171 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 GLN Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 770 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain B residue 1214 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 617 PHE Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 786 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 ASN Chi-restraints excluded: chain C residue 1136 PHE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 671 MET Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 356 optimal weight: 50.0000 chunk 118 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 443 optimal weight: 10.0000 chunk 454 optimal weight: 0.0970 chunk 217 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 384 optimal weight: 50.0000 chunk 194 optimal weight: 0.9990 chunk 349 optimal weight: 50.0000 chunk 337 optimal weight: 40.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1145 ASN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 808 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** 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 = 0.5335 r_free = 0.5335 target = 0.252995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5178 r_free = 0.5178 target = 0.239680 restraints weight = 134856.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5169 r_free = 0.5169 target = 0.239738 restraints weight = 164903.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.239704 restraints weight = 128465.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.239437 restraints weight = 97733.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.239697 restraints weight = 94028.131| |-----------------------------------------------------------------------------| r_work (final): 0.5183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3626 moved from start: 0.9432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37411 Z= 0.145 Angle : 0.675 22.953 50971 Z= 0.356 Chirality : 0.047 0.305 5558 Planarity : 0.005 0.109 6612 Dihedral : 5.456 49.007 5118 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.27 % Allowed : 18.04 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.15 (0.12), residues: 4643 helix: -0.41 (0.16), residues: 896 sheet: -0.52 (0.15), residues: 1180 loop : -0.95 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1069 TYR 0.040 0.002 TYR B 947 PHE 0.031 0.002 PHE B 788 TRP 0.028 0.001 TRP D 353 HIS 0.022 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00321 (37354) covalent geometry : angle 0.67266 (50857) SS BOND : bond 0.00466 ( 57) SS BOND : angle 1.46676 ( 114) hydrogen bonds : bond 0.04262 ( 1500) hydrogen bonds : angle 6.75494 ( 4071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 320 time to evaluate : 1.174 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 72 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: A 709 THR cc_start: 0.4714 (p) cc_final: 0.4448 (p) REVERT: A 757 MET cc_start: 0.1095 (mpp) cc_final: 0.0297 (mpp) REVERT: A 858 SER cc_start: 0.4969 (t) cc_final: 0.4468 (t) REVERT: A 1122 HIS cc_start: 0.3512 (t-90) cc_final: 0.2474 (t-170) REVERT: A 1171 TYR cc_start: 0.0209 (OUTLIER) cc_final: -0.2453 (m-80) REVERT: B 245 ILE cc_start: 0.4749 (mt) cc_final: 0.4327 (mm) REVERT: B 563 MET cc_start: -0.0256 (tpp) cc_final: -0.0908 (mmt) REVERT: B 1137 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.4772 (mmm) REVERT: B 1142 TYR cc_start: 0.4128 (OUTLIER) cc_final: 0.1760 (t80) REVERT: C 67 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6851 (mm) REVERT: C 240 MET cc_start: 0.4679 (mmt) cc_final: 0.4217 (mmt) REVERT: C 388 LEU cc_start: -0.0641 (OUTLIER) cc_final: -0.1216 (pt) REVERT: C 389 LEU cc_start: 0.0175 (OUTLIER) cc_final: -0.0444 (pt) REVERT: C 401 ARG cc_start: -0.1247 (OUTLIER) cc_final: -0.3505 (mtp180) REVERT: C 815 GLN cc_start: 0.5667 (mm-40) cc_final: 0.5289 (mm-40) REVERT: C 928 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.5288 (m-80) REVERT: C 943 MET cc_start: 0.5071 (tpp) cc_final: 0.4702 (tpt) REVERT: C 965 SER cc_start: 0.7630 (m) cc_final: 0.6841 (t) REVERT: D 68 TYR cc_start: 0.3345 (p90) cc_final: 0.2886 (p90) REVERT: D 132 TYR cc_start: 0.4114 (m-80) cc_final: 0.3527 (m-80) REVERT: D 187 TRP cc_start: 0.0953 (p-90) cc_final: -0.0454 (p-90) REVERT: D 322 TYR cc_start: 0.1829 (t80) cc_final: 0.0311 (m-80) REVERT: D 667 THR cc_start: 0.4902 (p) cc_final: 0.4634 (p) REVERT: D 761 GLN cc_start: 0.3859 (OUTLIER) cc_final: 0.3354 (mt0) REVERT: I 348 MET cc_start: 0.2386 (ptm) cc_final: 0.2149 (ptp) REVERT: I 573 ILE cc_start: 0.2894 (OUTLIER) cc_final: 0.2598 (tp) REVERT: I 651 ILE cc_start: 0.1761 (OUTLIER) cc_final: 0.1246 (tt) REVERT: I 715 GLN cc_start: -0.2518 (OUTLIER) cc_final: -0.2770 (mt0) outliers start: 89 outliers final: 64 residues processed: 387 average time/residue: 0.2127 time to fit residues: 137.3545 Evaluate side-chains 369 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 292 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1171 TYR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain C residue 862 ILE Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 361 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 408 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 217 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 438 optimal weight: 8.9990 chunk 133 optimal weight: 50.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 GLN B 618 GLN ** B 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 915 GLN B1016 ASN ** B1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 155 ASN C 766 HIS C 792 GLN C 815 GLN ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 HIS ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.249322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.235358 restraints weight = 132156.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.235763 restraints weight = 165829.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.235415 restraints weight = 125865.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.235265 restraints weight = 98074.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.235473 restraints weight = 86588.706| |-----------------------------------------------------------------------------| r_work (final): 0.5089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3808 moved from start: 0.9981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 37411 Z= 0.235 Angle : 0.778 30.470 50971 Z= 0.414 Chirality : 0.050 0.294 5558 Planarity : 0.006 0.111 6612 Dihedral : 5.840 48.877 5118 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.53 % Allowed : 18.04 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.12), residues: 4643 helix: -0.60 (0.16), residues: 886 sheet: -0.57 (0.15), residues: 1192 loop : -1.10 (0.12), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 190 TYR 0.068 0.002 TYR B 947 PHE 0.037 0.003 PHE B 266 TRP 0.025 0.002 TRP D 187 HIS 0.017 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00531 (37354) covalent geometry : angle 0.77382 (50857) SS BOND : bond 0.00693 ( 57) SS BOND : angle 1.91959 ( 114) hydrogen bonds : bond 0.04924 ( 1500) hydrogen bonds : angle 7.25153 ( 4071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9286 Ramachandran restraints generated. 4643 Oldfield, 0 Emsley, 4643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 291 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6365 (tm-30) REVERT: A 757 MET cc_start: 0.1021 (mpp) cc_final: 0.0576 (mpp) REVERT: A 858 SER cc_start: 0.5273 (t) cc_final: 0.4732 (t) REVERT: A 1000 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8050 (mmtt) REVERT: A 1171 TYR cc_start: 0.0390 (OUTLIER) cc_final: -0.2476 (m-80) REVERT: B 563 MET cc_start: -0.0230 (tpp) cc_final: -0.0795 (mmt) REVERT: B 1066 GLN cc_start: 0.5062 (tp-100) cc_final: 0.4304 (tp-100) REVERT: B 1142 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.2392 (t80) REVERT: C 111 GLN cc_start: 0.6873 (tp40) cc_final: 0.6452 (tp40) REVERT: C 240 MET cc_start: 0.4864 (mmt) cc_final: 0.4332 (mmt) REVERT: C 388 LEU cc_start: -0.0751 (OUTLIER) cc_final: -0.1320 (pt) REVERT: C 389 LEU cc_start: 0.0234 (OUTLIER) cc_final: -0.0476 (pt) REVERT: C 401 ARG cc_start: -0.1224 (OUTLIER) cc_final: -0.3460 (mtp180) REVERT: C 415 LEU cc_start: -0.1202 (OUTLIER) cc_final: -0.1778 (tp) REVERT: C 626 ARG cc_start: 0.2664 (OUTLIER) cc_final: 0.1565 (mmm160) REVERT: C 786 PHE cc_start: 0.3178 (OUTLIER) cc_final: 0.1863 (p90) REVERT: C 799 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.5643 (pt) REVERT: C 815 GLN cc_start: 0.6211 (mm110) cc_final: 0.5745 (mm-40) REVERT: C 928 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.5792 (m-80) REVERT: C 943 MET cc_start: 0.5430 (tpp) cc_final: 0.4916 (tpt) REVERT: C 1128 VAL cc_start: 0.0357 (OUTLIER) cc_final: -0.1409 (t) REVERT: D 68 TYR cc_start: 0.3341 (p90) cc_final: 0.2876 (p90) REVERT: D 115 LEU cc_start: 0.3913 (tt) cc_final: 0.3686 (tt) REVERT: D 187 TRP cc_start: 0.0891 (p-90) cc_final: -0.0381 (p-90) REVERT: D 322 TYR cc_start: 0.2263 (t80) cc_final: 0.0503 (m-10) REVERT: D 667 THR cc_start: 0.5023 (p) cc_final: 0.4761 (p) REVERT: D 761 GLN cc_start: 0.3850 (OUTLIER) cc_final: 0.3379 (mt0) REVERT: I 573 ILE cc_start: 0.2839 (OUTLIER) cc_final: 0.2561 (tp) REVERT: I 651 ILE cc_start: 0.1821 (OUTLIER) cc_final: 0.1282 (tt) REVERT: I 715 GLN cc_start: -0.2432 (OUTLIER) cc_final: -0.2676 (mt0) outliers start: 99 outliers final: 73 residues processed: 371 average time/residue: 0.2139 time to fit residues: 132.4569 Evaluate side-chains 367 residues out of total 4063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 278 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1171 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 635 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 799 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 940 ASP Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 972 PHE Chi-restraints excluded: chain B residue 1129 ASN Chi-restraints excluded: chain B residue 1137 MET Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1142 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 626 ARG Chi-restraints excluded: chain C residue 642 TYR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 764 PHE Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 786 PHE Chi-restraints excluded: chain C residue 795 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 803 THR Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 928 TYR Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 970 ILE Chi-restraints excluded: chain C residue 1106 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1137 MET Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 566 TYR Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 761 GLN Chi-restraints excluded: chain I residue 186 THR Chi-restraints excluded: chain I residue 341 VAL Chi-restraints excluded: chain I residue 566 TYR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 651 ILE Chi-restraints excluded: chain I residue 715 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 275 optimal weight: 2.9990 chunk 450 optimal weight: 50.0000 chunk 414 optimal weight: 0.0040 chunk 361 optimal weight: 50.0000 chunk 159 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 192 optimal weight: 0.5980 chunk 132 optimal weight: 0.0270 chunk 404 optimal weight: 20.0000 overall best weight: 0.6852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN B 681 HIS B 733 GLN B1016 ASN B1063 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.242130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.228883 restraints weight = 49671.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.223663 restraints weight = 75554.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.220826 restraints weight = 98774.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.219448 restraints weight = 122592.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5192 r_free = 0.5192 target = 0.218514 restraints weight = 111484.428| |-----------------------------------------------------------------------------| r_work (final): 0.5228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3491 moved from start: 0.9947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37411 Z= 0.135 Angle : 0.688 24.736 50971 Z= 0.359 Chirality : 0.047 0.253 5558 Planarity : 0.005 0.088 6612 Dihedral : 5.292 49.172 5118 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.74 % Allowed : 19.09 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.09 % 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: -1.09 (0.12), residues: 4643 helix: -0.37 (0.16), residues: 900 sheet: -0.50 (0.15), residues: 1175 loop : -0.91 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1069 TYR 0.041 0.002 TYR A 292 PHE 0.030 0.002 PHE C 764 TRP 0.023 0.001 TRP A 960 HIS 0.019 0.001 HIS A1122 Details of bonding type rmsd covalent geometry : bond 0.00298 (37354) covalent geometry : angle 0.68476 (50857) SS BOND : bond 0.00414 ( 57) SS BOND : angle 1.63634 ( 114) hydrogen bonds : bond 0.04110 ( 1500) hydrogen bonds : angle 6.59391 ( 4071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.17 seconds wall clock time: 93 minutes 37.96 seconds (5617.96 seconds total)