Starting phenix.real_space_refine on Tue Apr 7 13:00:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvg_34126/04_2026/7yvg_34126.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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 129 5.16 5 C 18192 2.51 5 N 4692 2.21 5 O 5466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 201 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28479 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7634 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 4, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 248 Chain: "B" Number of atoms: 7643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7643 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 301 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 10, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 242 Chain: "C" Number of atoms: 7649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7649 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 7 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 450 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 9, 'ASN:plan1': 9, 'GLU:plan': 11, 'PHE:plan': 3, 'ARG:plan': 9, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 237 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 818 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 865 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 6.34, per 1000 atoms: 0.22 Number of scatterers: 28479 At special positions: 0 Unit cell: (143.5, 147.6, 225.5, 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 129 16.00 O 5466 8.00 N 4692 7.00 C 18192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.01 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.06 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " 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: 1.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 50 sheets defined 21.1% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.858A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.775A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.522A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.077A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.525A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.199A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.813A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.778A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.595A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.524A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.012A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.192A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.988A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.904A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.533A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.162A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.097A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.789A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.030A pdb=" N SER H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 86 through 90 removed outlier: 4.092A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.002A pdb=" N SER J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 86 through 90 removed outlier: 4.046A pdb=" N THR K 90 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.122A pdb=" N SER L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.714A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.649A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.865A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.656A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.182A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.616A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.837A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.870A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.690A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.690A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.081A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.634A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.829A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.978A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.764A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.064A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 327 removed outlier: 5.672A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.538A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.909A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.614A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.614A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.369A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.527A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.522A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.935A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.077A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.669A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.521A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.620A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.811A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.658A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.911A pdb=" N GLY I 10 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.747A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.989A pdb=" N LEU J 11 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.972A pdb=" N GLY K 10 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.768A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.620A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.151A pdb=" N GLY M 10 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3255 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: 7.44 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6885 1.33 - 1.47: 10791 1.47 - 1.62: 11293 1.62 - 1.76: 50 1.76 - 1.91: 116 Bond restraints: 29135 Sorted by residual: bond pdb=" CG LEU I 4 " pdb=" CD2 LEU I 4 " ideal model delta sigma weight residual 1.521 1.730 -0.209 3.30e-02 9.18e+02 4.00e+01 bond pdb=" CB TRP B 886 " pdb=" CG TRP B 886 " ideal model delta sigma weight residual 1.498 1.346 0.152 3.10e-02 1.04e+03 2.41e+01 bond pdb=" C PRO A 862 " pdb=" O PRO A 862 " ideal model delta sigma weight residual 1.240 1.190 0.051 1.12e-02 7.97e+03 2.04e+01 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.667 0.141 3.30e-02 9.18e+02 1.82e+01 bond pdb=" C PRO A 863 " pdb=" O PRO A 863 " ideal model delta sigma weight residual 1.232 1.182 0.050 1.20e-02 6.94e+03 1.77e+01 ... (remaining 29130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 38572 3.35 - 6.71: 1093 6.71 - 10.06: 101 10.06 - 13.41: 26 13.41 - 16.77: 3 Bond angle restraints: 39795 Sorted by residual: angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 131.17 -16.77 2.30e+00 1.89e-01 5.31e+01 angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 129.51 -15.11 2.30e+00 1.89e-01 4.32e+01 angle pdb=" C SER H 30 " pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 122.14 111.20 10.94 1.67e+00 3.59e-01 4.29e+01 angle pdb=" C SER A 530 " pdb=" N THR A 531 " pdb=" CA THR A 531 " ideal model delta sigma weight residual 121.54 133.94 -12.40 1.91e+00 2.74e-01 4.21e+01 angle pdb=" N VAL A 367 " pdb=" CA VAL A 367 " pdb=" C VAL A 367 " ideal model delta sigma weight residual 111.81 106.48 5.33 8.60e-01 1.35e+00 3.84e+01 ... (remaining 39790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 16589 22.37 - 44.74: 856 44.74 - 67.11: 141 67.11 - 89.48: 49 89.48 - 111.85: 3 Dihedral angle restraints: 17638 sinusoidal: 6784 harmonic: 10854 Sorted by residual: dihedral pdb=" CA PRO J 95 " pdb=" C PRO J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -68.15 -111.85 0 5.00e+00 4.00e-02 5.00e+02 dihedral pdb=" CA PRO H 95 " pdb=" C PRO H 95 " pdb=" N PRO H 96 " pdb=" CA PRO H 96 " ideal model delta harmonic sigma weight residual -180.00 -68.58 -111.42 0 5.00e+00 4.00e-02 4.97e+02 dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual -180.00 -69.01 -110.99 0 5.00e+00 4.00e-02 4.93e+02 ... (remaining 17635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3790 0.099 - 0.197: 785 0.197 - 0.296: 78 0.296 - 0.394: 11 0.394 - 0.493: 6 Chirality restraints: 4670 Sorted by residual: chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA CYS A 166 " pdb=" N CYS A 166 " pdb=" C CYS A 166 " pdb=" CB CYS A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 4667 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.032 2.00e-02 2.50e+03 3.07e-02 2.35e+01 pdb=" CG TRP A 886 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 38 " 0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLN L 38 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN L 38 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS L 39 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 576 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C VAL B 576 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL B 576 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG B 577 " -0.024 2.00e-02 2.50e+03 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 545 2.63 - 3.20: 26794 3.20 - 3.77: 41289 3.77 - 4.33: 55666 4.33 - 4.90: 94357 Nonbonded interactions: 218651 Sorted by model distance: nonbonded pdb=" O SER L 77 " pdb=" NE2 GLN L 79 " model vdw 2.068 3.120 nonbonded pdb=" O THR I 28 " pdb=" ND2 ASN I 32 " model vdw 2.127 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O ASP C 467 " model vdw 2.149 3.120 nonbonded pdb=" OD1 ASN A 657 " pdb=" O6 NAG A1301 " model vdw 2.160 3.040 nonbonded pdb=" O LEU A 752 " pdb=" NE2 GLN A 755 " model vdw 2.161 3.120 ... (remaining 218646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 1311) selection = (chain 'B' and (resid 27 through 328 or (resid 329 and (name N or name CA or nam \ e C or name O or name CB )) or resid 330 through 532 or (resid 533 and (name N o \ r name CA or name C or name O or name CB )) or resid 534 through 1311)) selection = (chain 'C' and (resid 27 through 327 or (resid 328 through 329 and (name N or na \ me CA or name C or name O or name CB )) or resid 330 through 532 or (resid 533 a \ nd (name N or name CA or name C or name O or name CB )) or resid 534 through 131 \ 1)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.920 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.017 0.209 29180 Z= 0.693 Angle : 1.366 16.767 39885 Z= 0.745 Chirality : 0.080 0.493 4670 Planarity : 0.007 0.087 5097 Dihedral : 13.676 111.854 10537 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.52 % Favored : 94.02 % Rotamer: Outliers : 0.89 % Allowed : 7.39 % Favored : 91.72 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 3693 helix: 0.21 (0.20), residues: 647 sheet: -1.30 (0.14), residues: 979 loop : -2.46 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG M 86 TYR 0.054 0.004 TYR B 756 PHE 0.062 0.006 PHE A 565 TRP 0.072 0.005 TRP A 886 HIS 0.020 0.003 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01715 (29135) covalent geometry : angle 1.34303 (39795) SS BOND : bond 0.01190 ( 45) SS BOND : angle 5.47469 ( 90) hydrogen bonds : bond 0.14573 ( 1176) hydrogen bonds : angle 7.28604 ( 3255) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8271 (m-80) cc_final: 0.8010 (m-80) REVERT: A 394 ASN cc_start: 0.6944 (t0) cc_final: 0.6540 (p0) REVERT: A 765 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7448 (ttp-170) REVERT: A 774 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8281 (mp10) REVERT: B 135 PHE cc_start: 0.7033 (m-80) cc_final: 0.6669 (m-80) REVERT: B 957 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 140 PHE cc_start: 0.5203 (p90) cc_final: 0.4578 (p90) REVERT: C 754 LEU cc_start: 0.8792 (mm) cc_final: 0.8580 (mt) REVERT: C 979 ASP cc_start: 0.8801 (t70) cc_final: 0.8337 (t0) REVERT: C 984 LEU cc_start: 0.7919 (tp) cc_final: 0.7668 (mt) REVERT: J 94 TRP cc_start: 0.7006 (t-100) cc_final: 0.6584 (t-100) REVERT: M 34 MET cc_start: 0.4437 (mmt) cc_final: 0.3777 (tpt) REVERT: M 82 MET cc_start: 0.1521 (ptp) cc_final: -0.0602 (ttt) outliers start: 26 outliers final: 8 residues processed: 327 average time/residue: 0.1923 time to fit residues: 100.1191 Evaluate side-chains 199 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain C residue 551 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 343 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 506 GLN A 657 ASN A 954 HIS A 955 ASN A 978 ASN A1074 ASN A1098 ASN B 354 ASN B 388 ASN B 409 GLN B 506 GLN B 657 ASN B 856 ASN B 955 ASN B1010 GLN B1088 HIS C 99 ASN C 165 ASN C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 506 GLN C 540 ASN C 544 ASN C 657 ASN C 856 ASN C 949 GLN C1113 GLN C1134 ASN H 90 GLN I 3 GLN J 79 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 81 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.184210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113713 restraints weight = 50424.811| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.89 r_work: 0.3106 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29180 Z= 0.160 Angle : 0.704 11.921 39885 Z= 0.365 Chirality : 0.047 0.250 4670 Planarity : 0.005 0.108 5097 Dihedral : 6.829 59.931 4758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.47 % Favored : 95.42 % Rotamer: Outliers : 1.99 % Allowed : 11.58 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -1.33 (0.13), residues: 3693 helix: 1.39 (0.20), residues: 660 sheet: -0.53 (0.15), residues: 997 loop : -1.92 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.022 0.001 TYR H 98 PHE 0.027 0.002 PHE A 970 TRP 0.013 0.001 TRP B 436 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00372 (29135) covalent geometry : angle 0.69249 (39795) SS BOND : bond 0.00512 ( 45) SS BOND : angle 2.71790 ( 90) hydrogen bonds : bond 0.05391 ( 1176) hydrogen bonds : angle 5.85270 ( 3255) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8775 (m-80) cc_final: 0.8434 (m-80) REVERT: A 218 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 269 TYR cc_start: 0.7396 (m-80) cc_final: 0.6903 (m-80) REVERT: A 530 SER cc_start: 0.6850 (p) cc_final: 0.6488 (t) REVERT: A 574 ASP cc_start: 0.8521 (t70) cc_final: 0.8116 (t0) REVERT: A 754 LEU cc_start: 0.9424 (mm) cc_final: 0.8817 (pp) REVERT: A 964 LYS cc_start: 0.8584 (tppp) cc_final: 0.8032 (tmtt) REVERT: B 88 ASP cc_start: 0.8352 (m-30) cc_final: 0.8077 (m-30) REVERT: B 432 CYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6519 (m) REVERT: B 762 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 957 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8133 (tm-30) REVERT: C 30 ASN cc_start: 0.7283 (p0) cc_final: 0.6827 (m-40) REVERT: C 129 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7993 (tttm) REVERT: C 140 PHE cc_start: 0.5918 (p90) cc_final: 0.4880 (p90) REVERT: C 969 LYS cc_start: 0.9436 (mtpp) cc_final: 0.9229 (mmmm) REVERT: J 46 LEU cc_start: 0.6029 (tp) cc_final: 0.5755 (tp) REVERT: K 34 MET cc_start: 0.6536 (mmm) cc_final: 0.6175 (mmm) REVERT: M 34 MET cc_start: 0.4169 (mmt) cc_final: 0.3721 (tpt) REVERT: M 82 MET cc_start: 0.0896 (ptp) cc_final: -0.0470 (ttt) outliers start: 58 outliers final: 21 residues processed: 291 average time/residue: 0.1716 time to fit residues: 83.3740 Evaluate side-chains 204 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 242 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 246 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 186 optimal weight: 0.0570 chunk 4 optimal weight: 20.0000 chunk 368 optimal weight: 20.0000 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 314 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A1098 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.182189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110719 restraints weight = 50252.501| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.56 r_work: 0.3040 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 29180 Z= 0.219 Angle : 0.696 10.958 39885 Z= 0.361 Chirality : 0.048 0.244 4670 Planarity : 0.005 0.056 5097 Dihedral : 6.519 58.782 4747 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.96 % Allowed : 13.41 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % 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: -0.98 (0.13), residues: 3693 helix: 1.66 (0.20), residues: 660 sheet: -0.27 (0.15), residues: 1012 loop : -1.71 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.022 0.002 TYR B1067 PHE 0.029 0.002 PHE A 970 TRP 0.017 0.002 TRP J 35 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00538 (29135) covalent geometry : angle 0.68378 (39795) SS BOND : bond 0.00723 ( 45) SS BOND : angle 2.78848 ( 90) hydrogen bonds : bond 0.05844 ( 1176) hydrogen bonds : angle 5.74827 ( 3255) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 198 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8871 (m-80) cc_final: 0.8550 (m-80) REVERT: A 269 TYR cc_start: 0.7423 (m-80) cc_final: 0.7032 (m-80) REVERT: A 530 SER cc_start: 0.7119 (p) cc_final: 0.6817 (t) REVERT: A 574 ASP cc_start: 0.8570 (t70) cc_final: 0.8179 (t0) REVERT: A 754 LEU cc_start: 0.9453 (mm) cc_final: 0.8898 (pp) REVERT: A 964 LYS cc_start: 0.8641 (tppp) cc_final: 0.8130 (tmtt) REVERT: A 970 PHE cc_start: 0.8720 (m-80) cc_final: 0.8508 (m-10) REVERT: B 140 PHE cc_start: 0.6351 (p90) cc_final: 0.4612 (p90) REVERT: B 432 CYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6675 (m) REVERT: B 762 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7924 (mp10) REVERT: B 957 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 140 PHE cc_start: 0.5990 (p90) cc_final: 0.4863 (p90) REVERT: C 969 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9132 (mmmm) REVERT: C 994 ASP cc_start: 0.7790 (m-30) cc_final: 0.7553 (m-30) REVERT: J 46 LEU cc_start: 0.6306 (tp) cc_final: 0.5554 (tp) REVERT: J 102 GLN cc_start: 0.6859 (tp40) cc_final: 0.6385 (mp10) REVERT: K 34 MET cc_start: 0.6463 (mmm) cc_final: 0.6107 (mmm) REVERT: L 94 TRP cc_start: 0.6995 (t-100) cc_final: 0.6759 (t-100) REVERT: M 34 MET cc_start: 0.4484 (mmt) cc_final: 0.3864 (tpp) REVERT: M 82 MET cc_start: 0.1112 (ptp) cc_final: -0.0331 (ttt) outliers start: 86 outliers final: 50 residues processed: 266 average time/residue: 0.1653 time to fit residues: 74.1362 Evaluate side-chains 232 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 54 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 296 optimal weight: 0.4980 chunk 354 optimal weight: 30.0000 chunk 274 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 216 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.182327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110774 restraints weight = 50100.387| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.94 r_work: 0.3037 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29180 Z= 0.193 Angle : 0.664 18.088 39885 Z= 0.344 Chirality : 0.047 0.396 4670 Planarity : 0.005 0.057 5097 Dihedral : 6.272 56.768 4747 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.64 % Allowed : 14.37 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % 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: -0.81 (0.13), residues: 3693 helix: 1.86 (0.21), residues: 654 sheet: -0.13 (0.15), residues: 1010 loop : -1.64 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.002 PHE A 970 TRP 0.014 0.001 TRP J 35 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00467 (29135) covalent geometry : angle 0.65024 (39795) SS BOND : bond 0.00736 ( 45) SS BOND : angle 2.87691 ( 90) hydrogen bonds : bond 0.05415 ( 1176) hydrogen bonds : angle 5.58371 ( 3255) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 180 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8850 (m-80) cc_final: 0.8528 (m-80) REVERT: A 269 TYR cc_start: 0.7445 (m-80) cc_final: 0.7061 (m-80) REVERT: A 530 SER cc_start: 0.7177 (p) cc_final: 0.6878 (t) REVERT: A 574 ASP cc_start: 0.8589 (t70) cc_final: 0.8253 (t0) REVERT: A 754 LEU cc_start: 0.9441 (mm) cc_final: 0.8923 (pp) REVERT: B 88 ASP cc_start: 0.8343 (m-30) cc_final: 0.8114 (m-30) REVERT: B 432 CYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6630 (m) REVERT: B 762 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: B 957 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 140 PHE cc_start: 0.5896 (p90) cc_final: 0.4772 (p90) REVERT: C 480 CYS cc_start: 0.4269 (OUTLIER) cc_final: 0.4013 (p) REVERT: C 969 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9094 (mmmm) REVERT: C 994 ASP cc_start: 0.7752 (m-30) cc_final: 0.7511 (m-30) REVERT: H 104 THR cc_start: -0.1649 (OUTLIER) cc_final: -0.1928 (t) REVERT: K 34 MET cc_start: 0.6524 (mmm) cc_final: 0.6145 (mmm) REVERT: L 94 TRP cc_start: 0.7049 (t-100) cc_final: 0.6811 (t-100) REVERT: M 34 MET cc_start: 0.4545 (mmt) cc_final: 0.3955 (tpp) REVERT: M 82 MET cc_start: 0.1146 (ptp) cc_final: -0.0258 (ttt) outliers start: 106 outliers final: 71 residues processed: 265 average time/residue: 0.1518 time to fit residues: 69.6176 Evaluate side-chains 243 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 35 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 368 optimal weight: 50.0000 chunk 207 optimal weight: 0.3980 chunk 128 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 292 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 326 optimal weight: 40.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 949 GLN C 957 GLN H 90 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.182780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113140 restraints weight = 50241.922| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 5.29 r_work: 0.3071 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.128 Angle : 0.607 17.650 39885 Z= 0.315 Chirality : 0.045 0.375 4670 Planarity : 0.004 0.054 5097 Dihedral : 5.662 54.451 4747 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.51 % Allowed : 15.37 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3693 helix: 2.20 (0.21), residues: 651 sheet: 0.06 (0.15), residues: 983 loop : -1.56 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.020 0.001 TYR B1067 PHE 0.018 0.001 PHE B 329 TRP 0.014 0.001 TRP J 35 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00294 (29135) covalent geometry : angle 0.59326 (39795) SS BOND : bond 0.00541 ( 45) SS BOND : angle 2.74204 ( 90) hydrogen bonds : bond 0.04590 ( 1176) hydrogen bonds : angle 5.28274 ( 3255) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 186 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8745 (m-80) cc_final: 0.8480 (m-80) REVERT: A 269 TYR cc_start: 0.7115 (m-80) cc_final: 0.6762 (m-80) REVERT: A 574 ASP cc_start: 0.8359 (t70) cc_final: 0.8015 (t0) REVERT: A 754 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 88 ASP cc_start: 0.8151 (m-30) cc_final: 0.7945 (m-30) REVERT: B 169 GLU cc_start: 0.8311 (pm20) cc_final: 0.7955 (pp20) REVERT: B 200 TYR cc_start: 0.8721 (m-80) cc_final: 0.8491 (m-80) REVERT: B 432 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6632 (m) REVERT: B 957 GLN cc_start: 0.8206 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 30 ASN cc_start: 0.6970 (p0) cc_final: 0.6589 (m-40) REVERT: C 129 LYS cc_start: 0.8259 (tttm) cc_final: 0.7905 (tmtt) REVERT: C 140 PHE cc_start: 0.5820 (p90) cc_final: 0.4688 (p90) REVERT: C 480 CYS cc_start: 0.4099 (OUTLIER) cc_final: 0.3828 (p) REVERT: C 498 ARG cc_start: 0.7603 (ptp-170) cc_final: 0.6649 (mpt-90) REVERT: C 546 LEU cc_start: 0.7945 (tt) cc_final: 0.7412 (pp) REVERT: C 969 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9121 (mmmm) REVERT: C 994 ASP cc_start: 0.7523 (m-30) cc_final: 0.7259 (m-30) REVERT: H 4 MET cc_start: 0.3804 (ttt) cc_final: -0.0345 (pmm) REVERT: H 104 THR cc_start: -0.1883 (OUTLIER) cc_final: -0.2178 (t) REVERT: K 34 MET cc_start: 0.6595 (mmm) cc_final: 0.6275 (mmm) REVERT: L 94 TRP cc_start: 0.6956 (t-100) cc_final: 0.6682 (t-100) REVERT: M 34 MET cc_start: 0.4583 (mmt) cc_final: 0.4016 (tpp) REVERT: M 82 MET cc_start: 0.1011 (ptp) cc_final: -0.0339 (ttt) outliers start: 102 outliers final: 63 residues processed: 272 average time/residue: 0.1600 time to fit residues: 73.9532 Evaluate side-chains 239 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 346 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 249 optimal weight: 0.2980 chunk 238 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.183427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112559 restraints weight = 49368.670| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.58 r_work: 0.3007 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 29180 Z= 0.238 Angle : 0.681 11.422 39885 Z= 0.353 Chirality : 0.047 0.221 4670 Planarity : 0.005 0.057 5097 Dihedral : 5.979 54.971 4747 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 4.13 % Allowed : 15.57 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 2.05 % 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: -0.74 (0.14), residues: 3693 helix: 1.97 (0.21), residues: 650 sheet: 0.03 (0.15), residues: 992 loop : -1.66 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.022 0.002 TYR J 49 PHE 0.019 0.002 PHE B 329 TRP 0.011 0.001 TRP A 64 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00587 (29135) covalent geometry : angle 0.66903 (39795) SS BOND : bond 0.00616 ( 45) SS BOND : angle 2.72178 ( 90) hydrogen bonds : bond 0.05852 ( 1176) hydrogen bonds : angle 5.50607 ( 3255) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 189 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8861 (m-80) cc_final: 0.8631 (m-80) REVERT: A 269 TYR cc_start: 0.7410 (m-80) cc_final: 0.6918 (m-80) REVERT: A 544 ASN cc_start: 0.8976 (m-40) cc_final: 0.8333 (t0) REVERT: A 553 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8742 (p) REVERT: A 574 ASP cc_start: 0.8525 (t70) cc_final: 0.8198 (t0) REVERT: A 754 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8975 (pp) REVERT: A 950 ASP cc_start: 0.8225 (m-30) cc_final: 0.7995 (m-30) REVERT: B 88 ASP cc_start: 0.8336 (m-30) cc_final: 0.8112 (m-30) REVERT: B 169 GLU cc_start: 0.8368 (pm20) cc_final: 0.8024 (pp20) REVERT: B 200 TYR cc_start: 0.8791 (m-80) cc_final: 0.8552 (m-80) REVERT: B 432 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6808 (m) REVERT: B 957 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 129 LYS cc_start: 0.8277 (tttm) cc_final: 0.7897 (tmtt) REVERT: C 140 PHE cc_start: 0.5828 (p90) cc_final: 0.4575 (p90) REVERT: C 480 CYS cc_start: 0.4192 (OUTLIER) cc_final: 0.3932 (p) REVERT: C 498 ARG cc_start: 0.7575 (ptp-170) cc_final: 0.6535 (mpt-90) REVERT: C 546 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7738 (pp) REVERT: H 4 MET cc_start: 0.3242 (ttt) cc_final: -0.0385 (pmm) REVERT: H 104 THR cc_start: -0.1771 (OUTLIER) cc_final: -0.2077 (t) REVERT: K 20 LEU cc_start: 0.5456 (mt) cc_final: 0.5245 (mp) REVERT: K 34 MET cc_start: 0.6492 (mmm) cc_final: 0.6203 (mmm) REVERT: M 12 VAL cc_start: 0.2974 (m) cc_final: 0.2750 (m) REVERT: M 34 MET cc_start: 0.4773 (mmt) cc_final: 0.4225 (tpp) REVERT: M 82 MET cc_start: 0.1088 (ptp) cc_final: -0.0249 (ttt) outliers start: 120 outliers final: 89 residues processed: 283 average time/residue: 0.1557 time to fit residues: 75.3583 Evaluate side-chains 277 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 182 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 362 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 346 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 304 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 321 optimal weight: 0.3980 chunk 118 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 207 HIS C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.186389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115517 restraints weight = 49387.697| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 4.67 r_work: 0.3095 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.115 Angle : 0.598 17.909 39885 Z= 0.309 Chirality : 0.045 0.372 4670 Planarity : 0.004 0.056 5097 Dihedral : 5.390 54.529 4747 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 2.89 % Allowed : 17.33 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.49 (0.14), residues: 3693 helix: 2.28 (0.21), residues: 653 sheet: 0.17 (0.16), residues: 988 loop : -1.53 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 86 TYR 0.025 0.001 TYR C 170 PHE 0.017 0.001 PHE B 92 TRP 0.008 0.001 TRP L 94 HIS 0.004 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00255 (29135) covalent geometry : angle 0.58638 (39795) SS BOND : bond 0.00514 ( 45) SS BOND : angle 2.49978 ( 90) hydrogen bonds : bond 0.04382 ( 1176) hydrogen bonds : angle 5.18088 ( 3255) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 176 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7265 (m-80) cc_final: 0.6906 (m-80) REVERT: A 544 ASN cc_start: 0.8986 (m-40) cc_final: 0.8331 (t0) REVERT: A 553 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8757 (p) REVERT: A 574 ASP cc_start: 0.8498 (t70) cc_final: 0.8188 (t0) REVERT: A 582 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7442 (mt) REVERT: A 754 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8980 (pp) REVERT: A 1017 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8659 (tt0) REVERT: B 88 ASP cc_start: 0.8278 (m-30) cc_final: 0.8068 (m-30) REVERT: B 200 TYR cc_start: 0.8703 (m-80) cc_final: 0.8477 (m-80) REVERT: B 432 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6806 (m) REVERT: B 957 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 1141 LEU cc_start: 0.8779 (tp) cc_final: 0.8539 (tt) REVERT: C 129 LYS cc_start: 0.8252 (tttm) cc_final: 0.7884 (tmtt) REVERT: C 140 PHE cc_start: 0.5836 (p90) cc_final: 0.4622 (p90) REVERT: C 170 TYR cc_start: 0.7943 (t80) cc_final: 0.7450 (t80) REVERT: C 440 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8350 (mmmt) REVERT: C 480 CYS cc_start: 0.4087 (OUTLIER) cc_final: 0.3823 (p) REVERT: C 498 ARG cc_start: 0.7583 (ptp-170) cc_final: 0.6554 (mpt-90) REVERT: C 751 ASN cc_start: 0.9173 (m110) cc_final: 0.8718 (p0) REVERT: C 969 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9053 (mmmm) REVERT: H 104 THR cc_start: -0.1980 (OUTLIER) cc_final: -0.2261 (t) REVERT: J 4 MET cc_start: 0.5943 (mtt) cc_final: 0.5707 (mtp) REVERT: K 34 MET cc_start: 0.6539 (mmm) cc_final: 0.6306 (mmm) REVERT: M 34 MET cc_start: 0.4775 (mmt) cc_final: 0.4240 (tpp) REVERT: M 82 MET cc_start: 0.0969 (ptp) cc_final: -0.0398 (ttt) outliers start: 84 outliers final: 65 residues processed: 244 average time/residue: 0.1595 time to fit residues: 67.4458 Evaluate side-chains 241 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 170 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 353 optimal weight: 40.0000 chunk 113 optimal weight: 0.9980 chunk 363 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 40.0000 chunk 276 optimal weight: 0.9980 chunk 319 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN C 207 HIS C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.182580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112221 restraints weight = 50080.976| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.61 r_work: 0.3056 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29180 Z= 0.127 Angle : 0.590 12.747 39885 Z= 0.305 Chirality : 0.044 0.236 4670 Planarity : 0.004 0.053 5097 Dihedral : 5.184 54.141 4747 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.13 % Rotamer: Outliers : 3.33 % Allowed : 17.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.42 (0.14), residues: 3693 helix: 2.34 (0.21), residues: 654 sheet: 0.25 (0.16), residues: 998 loop : -1.51 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.021 0.001 TYR B1067 PHE 0.014 0.001 PHE K 52 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00298 (29135) covalent geometry : angle 0.58013 (39795) SS BOND : bond 0.00469 ( 45) SS BOND : angle 2.30907 ( 90) hydrogen bonds : bond 0.04454 ( 1176) hydrogen bonds : angle 5.12071 ( 3255) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 178 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7283 (m-80) cc_final: 0.6802 (m-80) REVERT: A 544 ASN cc_start: 0.9019 (m-40) cc_final: 0.8388 (t0) REVERT: A 553 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8720 (p) REVERT: A 574 ASP cc_start: 0.8453 (t70) cc_final: 0.8130 (t0) REVERT: A 582 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7422 (mt) REVERT: A 754 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8998 (pp) REVERT: B 88 ASP cc_start: 0.8245 (m-30) cc_final: 0.8041 (m-30) REVERT: B 200 TYR cc_start: 0.8714 (m-80) cc_final: 0.8472 (m-80) REVERT: B 432 CYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6753 (m) REVERT: B 957 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 1141 LEU cc_start: 0.8752 (tp) cc_final: 0.8518 (tt) REVERT: C 129 LYS cc_start: 0.8282 (tttm) cc_final: 0.7948 (tmtt) REVERT: C 140 PHE cc_start: 0.5793 (p90) cc_final: 0.4550 (p90) REVERT: C 380 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.2429 (m-80) REVERT: C 440 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8363 (mmmt) REVERT: C 480 CYS cc_start: 0.4010 (OUTLIER) cc_final: 0.3736 (p) REVERT: C 498 ARG cc_start: 0.7582 (ptp-170) cc_final: 0.6606 (mpt-90) REVERT: C 751 ASN cc_start: 0.9198 (m110) cc_final: 0.8723 (p0) REVERT: H 104 THR cc_start: -0.1967 (OUTLIER) cc_final: -0.2273 (t) REVERT: J 46 LEU cc_start: 0.6423 (tp) cc_final: 0.6176 (tp) REVERT: L 4 MET cc_start: 0.1123 (mmm) cc_final: 0.0635 (mmm) REVERT: M 34 MET cc_start: 0.4719 (mmt) cc_final: 0.4185 (tpp) REVERT: M 82 MET cc_start: 0.1016 (ptp) cc_final: -0.0315 (ttt) outliers start: 97 outliers final: 79 residues processed: 254 average time/residue: 0.1551 time to fit residues: 68.0901 Evaluate side-chains 257 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 265 optimal weight: 0.7980 chunk 351 optimal weight: 40.0000 chunk 82 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 329 optimal weight: 40.0000 chunk 120 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 336 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.183917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.113330 restraints weight = 50243.565| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.83 r_work: 0.3114 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29180 Z= 0.126 Angle : 0.597 19.315 39885 Z= 0.308 Chirality : 0.044 0.324 4670 Planarity : 0.004 0.052 5097 Dihedral : 5.073 54.121 4747 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.68 % Favored : 95.29 % Rotamer: Outliers : 3.51 % Allowed : 17.46 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.35 (0.14), residues: 3693 helix: 2.40 (0.21), residues: 653 sheet: 0.27 (0.16), residues: 1011 loop : -1.47 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.026 0.001 TYR C 170 PHE 0.014 0.001 PHE A 970 TRP 0.014 0.001 TRP B 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00296 (29135) covalent geometry : angle 0.58741 (39795) SS BOND : bond 0.00492 ( 45) SS BOND : angle 2.35661 ( 90) hydrogen bonds : bond 0.04403 ( 1176) hydrogen bonds : angle 5.06482 ( 3255) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 171 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7290 (m-80) cc_final: 0.6832 (m-80) REVERT: A 544 ASN cc_start: 0.9009 (m-40) cc_final: 0.8479 (t0) REVERT: A 553 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8816 (p) REVERT: A 574 ASP cc_start: 0.8495 (t70) cc_final: 0.8261 (t0) REVERT: A 582 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7509 (mt) REVERT: A 754 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 1017 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8580 (tt0) REVERT: B 88 ASP cc_start: 0.8229 (m-30) cc_final: 0.8002 (m-30) REVERT: B 200 TYR cc_start: 0.8684 (m-80) cc_final: 0.8458 (m-80) REVERT: B 957 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 1141 LEU cc_start: 0.8805 (tp) cc_final: 0.8555 (tt) REVERT: C 129 LYS cc_start: 0.8322 (tttm) cc_final: 0.7973 (tmtt) REVERT: C 140 PHE cc_start: 0.5780 (p90) cc_final: 0.4493 (p90) REVERT: C 226 LEU cc_start: 0.7510 (mt) cc_final: 0.6900 (pp) REVERT: C 380 TYR cc_start: 0.4599 (OUTLIER) cc_final: 0.2669 (m-80) REVERT: C 440 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8335 (mmmt) REVERT: C 480 CYS cc_start: 0.3985 (OUTLIER) cc_final: 0.3710 (p) REVERT: C 498 ARG cc_start: 0.7576 (ptp-170) cc_final: 0.6570 (mpt-90) REVERT: C 546 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7781 (pp) REVERT: C 751 ASN cc_start: 0.9130 (m110) cc_final: 0.8679 (p0) REVERT: H 104 THR cc_start: -0.1963 (OUTLIER) cc_final: -0.2251 (t) REVERT: J 46 LEU cc_start: 0.6490 (tp) cc_final: 0.6229 (tp) REVERT: L 4 MET cc_start: 0.0826 (mmm) cc_final: 0.0315 (mmm) REVERT: M 34 MET cc_start: 0.4707 (mmt) cc_final: 0.4186 (tpp) REVERT: M 82 MET cc_start: 0.0996 (ptp) cc_final: -0.0370 (ttt) outliers start: 102 outliers final: 84 residues processed: 253 average time/residue: 0.1556 time to fit residues: 67.8374 Evaluate side-chains 258 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 167 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 949 GLN Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 27 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 197 optimal weight: 0.0370 chunk 323 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 167 optimal weight: 0.0980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 949 GLN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.185082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114741 restraints weight = 49893.580| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.95 r_work: 0.3141 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29180 Z= 0.109 Angle : 0.585 19.442 39885 Z= 0.301 Chirality : 0.044 0.381 4670 Planarity : 0.004 0.049 5097 Dihedral : 4.840 53.851 4747 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.49 % Favored : 95.48 % Rotamer: Outliers : 2.89 % Allowed : 18.01 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.23 (0.14), residues: 3693 helix: 2.53 (0.21), residues: 653 sheet: 0.38 (0.16), residues: 1002 loop : -1.40 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 983 TYR 0.021 0.001 TYR K 94 PHE 0.015 0.001 PHE B 92 TRP 0.012 0.001 TRP J 35 HIS 0.003 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00236 (29135) covalent geometry : angle 0.57461 (39795) SS BOND : bond 0.00472 ( 45) SS BOND : angle 2.33901 ( 90) hydrogen bonds : bond 0.03991 ( 1176) hydrogen bonds : angle 4.92161 ( 3255) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 186 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 TYR cc_start: 0.7237 (m-80) cc_final: 0.6837 (m-80) REVERT: A 544 ASN cc_start: 0.9034 (m-40) cc_final: 0.8479 (t0) REVERT: A 553 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8823 (p) REVERT: A 574 ASP cc_start: 0.8591 (t70) cc_final: 0.8323 (t0) REVERT: A 582 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 754 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9054 (pp) REVERT: A 1017 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8577 (tt0) REVERT: B 200 TYR cc_start: 0.8646 (m-80) cc_final: 0.8411 (m-80) REVERT: B 957 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 1141 LEU cc_start: 0.8780 (tp) cc_final: 0.8547 (tt) REVERT: C 129 LYS cc_start: 0.8349 (tttm) cc_final: 0.8034 (tmtt) REVERT: C 140 PHE cc_start: 0.5744 (p90) cc_final: 0.4431 (p90) REVERT: C 170 TYR cc_start: 0.7958 (t80) cc_final: 0.7561 (t80) REVERT: C 380 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.3165 (m-80) REVERT: C 440 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8346 (mmmt) REVERT: C 480 CYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3660 (p) REVERT: C 498 ARG cc_start: 0.7574 (ptp-170) cc_final: 0.6648 (mpt-90) REVERT: C 751 ASN cc_start: 0.9125 (m110) cc_final: 0.8689 (p0) REVERT: C 969 LYS cc_start: 0.9351 (mtpp) cc_final: 0.9049 (mmmm) REVERT: H 104 THR cc_start: -0.1978 (OUTLIER) cc_final: -0.2267 (t) REVERT: J 46 LEU cc_start: 0.6451 (tp) cc_final: 0.6212 (tp) REVERT: L 4 MET cc_start: 0.0840 (mmm) cc_final: 0.0323 (mmm) REVERT: M 34 MET cc_start: 0.4860 (mmt) cc_final: 0.4267 (tpp) REVERT: M 82 MET cc_start: 0.1025 (ptp) cc_final: -0.0338 (ttt) outliers start: 84 outliers final: 67 residues processed: 253 average time/residue: 0.1553 time to fit residues: 67.0676 Evaluate side-chains 249 residues out of total 3234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 176 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain K residue 52 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 89 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 154 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 259 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 317 optimal weight: 40.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 405 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.184028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113384 restraints weight = 50006.340| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 4.86 r_work: 0.3118 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29180 Z= 0.127 Angle : 0.595 16.848 39885 Z= 0.306 Chirality : 0.044 0.343 4670 Planarity : 0.004 0.051 5097 Dihedral : 4.825 54.115 4747 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.79 % Favored : 95.18 % Rotamer: Outliers : 2.89 % Allowed : 18.05 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 1.54 % 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: -0.23 (0.14), residues: 3693 helix: 2.53 (0.21), residues: 652 sheet: 0.38 (0.16), residues: 1005 loop : -1.41 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 983 TYR 0.022 0.001 TYR B1067 PHE 0.019 0.001 PHE K 58 TRP 0.014 0.001 TRP L 94 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00297 (29135) covalent geometry : angle 0.58528 (39795) SS BOND : bond 0.00448 ( 45) SS BOND : angle 2.37235 ( 90) hydrogen bonds : bond 0.04353 ( 1176) hydrogen bonds : angle 4.96271 ( 3255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10662.91 seconds wall clock time: 181 minutes 51.03 seconds (10911.03 seconds total)