Starting phenix.real_space_refine on Wed May 28 18:29:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410.map" model { file = "/net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h07_34410/05_2025/8h07_34410_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.065 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 131 5.16 5 C 19807 2.51 5 N 5330 2.21 5 O 6052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "O ASP 105": not complete - not flipped Residue "K ASP 105": not complete - not flipped Residue "R ASP 105": not complete - not flipped Time to flip 69 residue(s): 0.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31320 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 939, 7115 Classifications: {'peptide': 939} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 51, 'TRANS': 887} Chain breaks: 12 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7139 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 51, 'TRANS': 896} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 161 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7188 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 52, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "E" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 837 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 739 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 847 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 741 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "K" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "M" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 838 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 743 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Q" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 18.54, per 1000 atoms: 0.59 Number of scatterers: 31320 At special positions: 0 Unit cell: (161.02, 172.66, 218.25, 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 131 16.00 O 6052 8.00 N 5330 7.00 C 19807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=1.65 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.12 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=1.65 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.27 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.65 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 93 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B1301 " - " ASN B 343 " " NAG C1301 " - " ASN C 343 " Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 4.1 seconds 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7722 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 76 sheets defined 17.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 removed outlier: 4.574A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.824A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.599A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.150A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.529A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.940A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.666A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.613A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.557A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.723A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 4.575A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.824A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.535A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 4.347A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.581A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.550A pdb=" N THR B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.345A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.510A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.525A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.710A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.873A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.575A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.824A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.996A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 758 through 779 removed outlier: 3.588A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.617A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.737A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.789A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.705A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 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 984 removed outlier: 3.701A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1022 removed outlier: 3.531A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.636A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.784A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 96 removed outlier: 3.919A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.810A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.213A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.527A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.984A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.512A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.890A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1098 removed outlier: 4.273A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.898A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 117 through 118 removed outlier: 3.798A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.982A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 327 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.666A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.567A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.774A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.550A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD3, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 30 removed outlier: 4.147A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.013A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.972A pdb=" N PHE C 106 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.961A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.658A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.665A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.826A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.347A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.547A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE6, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE8, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL E 94 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET E 32 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL E 48 " --> pdb=" O MET E 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF3, first strand: chain 'J' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'N' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN N 39 " --> pdb=" O LEU N 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.571A pdb=" N PHE O 71 " --> pdb=" O CYS O 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER O 67 " --> pdb=" O ASP O 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG O 63 " --> pdb=" O THR O 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'O' and resid 53 through 54 removed outlier: 6.238A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL G 94 " --> pdb=" O SER G 33 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET G 32 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL G 48 " --> pdb=" O MET G 32 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG5, first strand: chain 'H' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AG8, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN I 39 " --> pdb=" O LEU I 93 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.571A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.238A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.546A pdb=" N VAL M 94 " --> pdb=" O SER M 33 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N MET M 32 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL M 48 " --> pdb=" O MET M 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP M 34 " --> pdb=" O VAL M 46 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AH7, first strand: chain 'P' and resid 45 through 48 removed outlier: 5.800A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AH9, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AI1, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.144A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN Q 39 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 4 through 6 removed outlier: 3.572A pdb=" N PHE R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER R 67 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG R 63 " --> pdb=" O THR R 74 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AI4, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.239A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2865 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: 15.24 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5182 1.31 - 1.44: 8969 1.44 - 1.57: 17716 1.57 - 1.70: 0 1.70 - 1.83: 162 Bond restraints: 32029 Sorted by residual: bond pdb=" CA SER B 438 " pdb=" CB SER B 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.32e+01 bond pdb=" CA SER C 438 " pdb=" CB SER C 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.32e+01 bond pdb=" CA SER A 438 " pdb=" CB SER A 438 " ideal model delta sigma weight residual 1.527 1.462 0.065 7.60e-03 1.73e+04 7.30e+01 bond pdb=" C VAL A 62 " pdb=" N THR A 63 " ideal model delta sigma weight residual 1.331 1.428 -0.098 1.31e-02 5.83e+03 5.57e+01 bond pdb=" CA SER B 673 " pdb=" CB SER B 673 " ideal model delta sigma weight residual 1.538 1.456 0.082 1.22e-02 6.72e+03 4.55e+01 ... (remaining 32024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.71: 43238 5.71 - 11.42: 368 11.42 - 17.14: 18 17.14 - 22.85: 0 22.85 - 28.56: 1 Bond angle restraints: 43625 Sorted by residual: angle pdb=" C THR C1077 " pdb=" CA THR C1077 " pdb=" CB THR C1077 " ideal model delta sigma weight residual 109.56 81.00 28.56 2.22e+00 2.03e-01 1.65e+02 angle pdb=" C CYS B1082 " pdb=" CA CYS B1082 " pdb=" CB CYS B1082 " ideal model delta sigma weight residual 109.90 95.05 14.85 1.56e+00 4.11e-01 9.06e+01 angle pdb=" N LYS A 814 " pdb=" CA LYS A 814 " pdb=" C LYS A 814 " ideal model delta sigma weight residual 113.02 102.57 10.45 1.20e+00 6.94e-01 7.59e+01 angle pdb=" N PRO B 812 " pdb=" CA PRO B 812 " pdb=" C PRO B 812 " ideal model delta sigma weight residual 113.47 101.04 12.43 1.43e+00 4.89e-01 7.55e+01 angle pdb=" C LYS A 440 " pdb=" CA LYS A 440 " pdb=" CB LYS A 440 " ideal model delta sigma weight residual 110.79 96.81 13.98 1.68e+00 3.54e-01 6.92e+01 ... (remaining 43620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 18077 24.33 - 48.67: 785 48.67 - 73.00: 120 73.00 - 97.34: 7 97.34 - 121.67: 3 Dihedral angle restraints: 18992 sinusoidal: 6940 harmonic: 12052 Sorted by residual: dihedral pdb=" C TYR K 94 " pdb=" N TYR K 94 " pdb=" CA TYR K 94 " pdb=" CB TYR K 94 " ideal model delta harmonic sigma weight residual -122.60 -157.52 34.92 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C TYR O 94 " pdb=" N TYR O 94 " pdb=" CA TYR O 94 " pdb=" CB TYR O 94 " ideal model delta harmonic sigma weight residual -122.60 -157.51 34.91 0 2.50e+00 1.60e-01 1.95e+02 dihedral pdb=" C TYR R 94 " pdb=" N TYR R 94 " pdb=" CA TYR R 94 " pdb=" CB TYR R 94 " ideal model delta harmonic sigma weight residual -122.60 -157.46 34.86 0 2.50e+00 1.60e-01 1.94e+02 ... (remaining 18989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 4770 0.289 - 0.577: 147 0.577 - 0.866: 1 0.866 - 1.154: 0 1.154 - 1.443: 3 Chirality restraints: 4921 Sorted by residual: chirality pdb=" CA TYR K 94 " pdb=" N TYR K 94 " pdb=" C TYR K 94 " pdb=" CB TYR K 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CA TYR O 94 " pdb=" N TYR O 94 " pdb=" C TYR O 94 " pdb=" CB TYR O 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CA TYR R 94 " pdb=" N TYR R 94 " pdb=" C TYR R 94 " pdb=" CB TYR R 94 " both_signs ideal model delta sigma weight residual False 2.51 1.07 1.44 2.00e-01 2.50e+01 5.18e+01 ... (remaining 4918 not shown) Planarity restraints: 5690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " 0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 479 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO B 479 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 478 " 0.072 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 479 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.064 5.00e-02 4.00e+02 ... (remaining 5687 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4333 2.76 - 3.29: 29175 3.29 - 3.83: 46429 3.83 - 4.36: 62481 4.36 - 4.90: 101340 Nonbonded interactions: 243758 Sorted by model distance: nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASN B 122 " pdb=" O ASN B 125 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN B 122 " pdb=" N ASN B 125 " model vdw 2.312 3.120 nonbonded pdb=" O THR B1077 " pdb=" OG1 THR B1077 " model vdw 2.339 3.040 nonbonded pdb=" N MET A 902 " pdb=" O MET A 902 " model vdw 2.348 2.496 ... (remaining 243753 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 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 41 or (resid 42 through 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or r \ esid 65 or resid 89 through 95 or (resid 101 and (name N or name CA or name C or \ name O or name CB )) or resid 102 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 118 or (resid 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 130 o \ r resid 189 through 194 or (resid 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 207 or resid 216 through 226 or (resid 227 a \ nd (name N or name CA or name C or name O or name CB )) or resid 228 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 238 and (name N or name CA or name C or n \ ame O or name CB )) or resid 239 through 241 or resid 264 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 308 or (resid 309 through 310 and (name N or name CA or name C or name O or na \ me CB )) or resid 311 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 528 or (resid 529 through 530 and \ (name N or name CA or name C or name O or name CB )) or resid 531 through 538 or \ (resid 539 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 0 through 548 or (resid 549 and (name N or name CA or name C or name O or name C \ B )) or resid 550 through 564 or (resid 565 and (name N or name CA or name C or \ name O or name CB )) or resid 566 through 573 or (resid 574 through 575 and (nam \ e N or name CA or name C or name O or name CB )) or resid 576 through 577 or (re \ sid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 or \ (resid 580 through 581 and (name N or name CA or name C or name O or name CB )) \ or resid 582 through 591 or (resid 592 and (name N or name CA or name C or name \ O or name CB )) or resid 593 through 607 or (resid 608 through 609 and (name N \ or name CA or name C or name O or name CB )) or resid 610 through 615 or (resid \ 616 and (name N or name CA or name C or name O or name CB )) or resid 617 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 643 or (resid 644 through 647 and (name N or name CA or name C \ or name O or name CB )) or resid 648 through 659 or (resid 660 and (name N or n \ ame CA or name C or name O or name CB )) or resid 661 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 66 \ 5 or (resid 666 and (name N or name CA or name C or name O or name CB )) or (res \ id 667 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 675 or resid 691 through 704 or (resid 705 through 707 and (nam \ e N or name CA or name C or name O or name CB )) or resid 708 through 710 or (re \ sid 711 through 714 and (name N or name CA or name C or name O or name CB )) or \ resid 715 through 721 or (resid 722 and (name N or name CA or name C or name O o \ r name CB )) or resid 723 through 750 or (resid 751 and (name N or name CA or na \ me C or name O or name CB )) or resid 752 through 779 or (resid 780 and (name N \ or name CA or name C or name O or name CB )) or resid 781 through 785 or (resid \ 786 and (name N or name CA or name C or name O or name CB )) or resid 787 throug \ h 789 or (resid 790 and (name N or name CA or name C or name O or name CB )) or \ resid 791 through 804 or (resid 805 and (name N or name CA or name C or name O o \ r name CB )) or resid 806 through 807 or (resid 808 and (name N or name CA or na \ me C or name O or name CB )) or resid 809 through 810 or (resid 811 and (name N \ or name CA or name C or name O or name CB )) or resid 812 through 825 or (resid \ 826 through 855 and (name N or name CA or name C or name O or name CB )) or resi \ d 856 through 857 or (resid 858 and (name N or name CA or name C or name O or na \ me CB )) or resid 859 through 882 or (resid 883 and (name N or name CA or name C \ or name O or name CB )) or resid 884 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 through 914 or (resid 915 \ through 917 and (name N or name CA or name C or name O or name CB )) or resid 91 \ 8 through 933 or (resid 934 through 935 and (name N or name CA or name C or name \ O or name CB )) or resid 936 through 937 or (resid 938 and (name N or name CA o \ r name C or name O or name CB )) or resid 939 through 968 or (resid 969 and (nam \ e N or name CA or name C or name O or name CB )) or resid 970 through 972 or (re \ sid 973 and (name N or name CA or name C or name O or name CB )) or resid 974 th \ rough 983 or (resid 984 and (name N or name CA or name C or name O or name CB )) \ or resid 985 through 995 or (resid 996 through 997 and (name N or name CA or na \ me C or name O or name CB )) or resid 998 through 1003 or (resid 1004 and (name \ N or name CA or name C or name O or name CB )) or resid 1005 through 1064 or (re \ sid 1065 and (name N or name CA or name C or name O or name CB )) or resid 1066 \ through 1071 or (resid 1072 and (name N or name CA or name C or name O or name C \ B )) or resid 1073 through 1074 or (resid 1075 and (name N or name CA or name C \ or name O or name CB )) or resid 1076 through 1103 or (resid 1104 and (name N or \ name CA or name C or name O or name CB )) or resid 1105 or (resid 1106 through \ 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 thro \ ugh 1118 or (resid 1119 through 1122 and (name N or name CA or name C or name O \ or name CB )) or resid 1123 through 1131 or (resid 1132 and (name N or name CA o \ r name C or name O or name CB )) or resid 1133 through 1136 or (resid 1137 and ( \ name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 27 through 41 or (resid 42 through 43 and (name N or name \ CA or name C or name O or name CB )) or resid 44 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 95 or (res \ id 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thr \ ough 103 or (resid 104 through 105 and (name N or name CA or name C or name O or \ name CB )) or resid 106 through 107 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 or (resid 119 and (name N or name CA or \ name C or name O or name CB )) or resid 120 or resid 126 through 129 or (resid \ 130 and (name N or name CA or name C or name O or name CB )) or resid 189 throug \ h 196 or (resid 201 and (name N or name CA or name C or name O or name CB )) or \ resid 202 through 205 or (resid 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 or resid 216 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 or (resid 229 and (name N \ or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and (na \ me N or name CA or name C or name O or name CB )) or resid 232 through 234 or (r \ esid 235 through 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 240 or (resid 241 through 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 266 or (resid 267 and (name N or \ name CA or name C or name O or name CB )) or resid 268 through 318 or (resid 319 \ and (name N or name CA or name C or name O or name CB )) or resid 320 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 528 or (resid 529 through 530 and (name N or name CA or name C or \ name O or name CB )) or resid 531 through 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 538 or (resid 539 and \ (name N or name CA or name C or name O or name CB )) or resid 540 through 543 o \ r (resid 544 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 45 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 583 or (resid 584 and (name N or name \ CA or name C or name O or name CB )) or resid 585 through 586 or (resid 587 and \ (name N or name CA or name C or name O or name CB )) or resid 588 through 598 o \ r (resid 599 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 00 through 645 or (resid 646 through 647 and (name N or name CA or name C or nam \ e O or name CB )) or resid 648 through 665 or (resid 666 and (name N or name CA \ or name C or name O or name CB )) or resid 667 through 675 or resid 691 through \ 706 or (resid 707 and (name N or name CA or name C or name O or name CB )) or re \ sid 708 through 713 or (resid 714 and (name N or name CA or name C or name O or \ name CB )) or resid 715 through 721 or (resid 722 and (name N or name CA or name \ C or name O or name CB )) or resid 723 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 through 779 or (resid 78 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 781 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or re \ sid 787 through 803 or (resid 804 through 805 and (name N or name CA or name C o \ r name O or name CB )) or resid 806 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 812 through 813 or (resid 814 an \ d (name N or name CA or name C or name O or name CB )) or resid 815 or (resid 81 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 817 through \ 826 or (resid 855 and (name N or name CA or name C or name O or name CB )) or re \ sid 856 through 857 or (resid 858 and (name N or name CA or name C or name O or \ name CB )) or resid 859 through 894 or (resid 895 and (name N or name CA or name \ C or name O or name CB )) or resid 896 through 901 or (resid 902 through 904 an \ d (name N or name CA or name C or name O or name CB )) or resid 905 through 911 \ or (resid 912 and (name N or name CA or name C or name O or name CB )) or resid \ 913 through 914 or (resid 915 through 917 and (name N or name CA or name C or na \ me O or name CB )) or resid 918 through 933 or (resid 934 through 935 and (name \ N or name CA or name C or name O or name CB )) or resid 936 through 944 or (resi \ d 945 and (name N or name CA or name C or name O or name CB )) or resid 946 thro \ ugh 968 or (resid 969 and (name N or name CA or name C or name O or name CB )) o \ r resid 970 through 972 or (resid 973 and (name N or name CA or name C or name O \ or name CB )) or resid 974 through 983 or (resid 984 and (name N or name CA or \ name C or name O or name CB )) or resid 985 through 986 or resid 988 through 996 \ or (resid 997 and (name N or name CA or name C or name O or name CB )) or resid \ 998 through 1028 or (resid 1029 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1030 through 1033 or (resid 1034 and (name N or name CA or na \ me C or name O or name CB )) or resid 1035 through 1076 or (resid 1077 through 1 \ 078 and (name N or name CA or name C or name O or name CB )) or resid 1079 throu \ gh 1095 or (resid 1096 and (name N or name CA or name C or name O or name CB )) \ or resid 1097 through 1118 or (resid 1119 through 1122 and (name N or name CA or \ name C or name O or name CB )) or resid 1123 through 1136 or (resid 1137 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'C' and (resid 27 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 63 or (resid 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 or resid 89 or (resid 90 and \ (name N or name CA or name C or name O or name CB )) or resid 91 through 103 or \ (resid 104 through 105 and (name N or name CA or name C or name O or name CB )) \ or resid 106 through 107 or resid 117 through 120 or resid 126 through 127 or (r \ esid 128 and (name N or name CA or name C or name O or name CB )) or resid 129 o \ r (resid 130 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 89 through 194 or (resid 195 and (name N or name CA or name C or name O or name \ CB )) or resid 196 or (resid 201 and (name N or name CA or name C or name O or n \ ame CB )) or resid 202 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 230 or (resid 231 and (name N or \ name CA or name C or name O or name CB )) or resid 232 through 236 or (resid 237 \ through 238 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 39 through 241 or resid 263 or resid 265 through 266 or (resid 267 and (name N o \ r name CA or name C or name O or name CB )) or resid 268 through 303 or (resid 3 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 305 through \ 308 or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or resid 311 through 529 or (resid 530 and (name N or name CA or name C \ or name O or name CB )) or resid 531 through 533 or (resid 534 and (name N or na \ me CA or name C or name O or name CB )) or resid 535 through 548 or (resid 549 a \ nd (name N or name CA or name C or name O or name CB )) or resid 550 through 559 \ or (resid 560 and (name N or name CA or name C or name O or name CB )) or resid \ 561 through 564 or (resid 565 and (name N or name CA or name C or name O or nam \ e CB )) or resid 566 through 567 or (resid 568 and (name N or name CA or name C \ or name O or name CB )) or resid 569 through 573 or (resid 574 through 575 and ( \ name N or name CA or name C or name O or name CB )) or resid 576 through 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 \ or (resid 580 through 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 through 586 or (resid 587 and (name N or name CA or name C or n \ ame O or name CB )) or resid 588 through 591 or (resid 592 and (name N or name C \ A or name C or name O or name CB )) or resid 593 through 598 or (resid 599 and ( \ name N or name CA or name C or name O or name CB )) or resid 600 through 607 or \ (resid 608 through 609 and (name N or name CA or name C or name O or name CB )) \ or resid 610 through 615 or (resid 616 and (name N or name CA or name C or name \ O or name CB )) or resid 617 through 618 or (resid 619 and (name N or name CA or \ name C or name O or name CB )) or resid 620 through 643 or (resid 644 through 6 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 648 through \ 659 or (resid 660 and (name N or name CA or name C or name O or name CB )) or r \ esid 661 through 662 or (resid 663 and (name N or name CA or name C or name O or \ name CB )) or resid 664 through 669 or (resid 670 and (name N or name CA or nam \ e C or name O or name CB )) or resid 671 through 704 or (resid 705 through 707 a \ nd (name N or name CA or name C or name O or name CB )) or resid 708 through 710 \ or (resid 711 through 714 and (name N or name CA or name C or name O or name CB \ )) or resid 715 through 725 or (resid 726 and (name N or name CA or name C or n \ ame O or name CB )) or resid 727 through 750 or (resid 751 and (name N or name C \ A or name C or name O or name CB )) or resid 752 through 754 or (resid 755 and ( \ name N or name CA or name C or name O or name CB )) or resid 756 through 789 or \ (resid 790 and (name N or name CA or name C or name O or name CB )) or resid 791 \ through 803 or (resid 804 through 805 and (name N or name CA or name C or name \ O or name CB )) or resid 806 through 807 or (resid 808 and (name N or name CA or \ name C or name O or name CB )) or resid 809 through 815 or (resid 816 and (name \ N or name CA or name C or name O or name CB )) or resid 817 through 825 or (res \ id 826 through 855 and (name N or name CA or name C or name O or name CB )) or r \ esid 856 through 882 or (resid 883 and (name N or name CA or name C or name O or \ name CB )) or resid 884 through 893 or (resid 894 through 895 and (name N or na \ me CA or name C or name O or name CB )) or resid 896 through 901 or (resid 902 t \ hrough 904 and (name N or name CA or name C or name O or name CB )) or resid 905 \ through 908 or (resid 909 and (name N or name CA or name C or name O or name CB \ )) or resid 910 through 911 or (resid 912 and (name N or name CA or name C or n \ ame O or name CB )) or resid 913 through 915 or (resid 916 through 917 and (name \ N or name CA or name C or name O or name CB )) or resid 918 through 937 or (res \ id 938 and (name N or name CA or name C or name O or name CB )) or resid 939 thr \ ough 944 or (resid 945 and (name N or name CA or name C or name O or name CB )) \ or resid 946 through 986 or resid 988 through 995 or (resid 996 through 997 and \ (name N or name CA or name C or name O or name CB )) or resid 998 through 1003 o \ r (resid 1004 and (name N or name CA or name C or name O or name CB )) or resid \ 1005 through 1049 or (resid 1050 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1051 through 1064 or (resid 1065 and (name N or name CA or na \ me C or name O or name CB )) or resid 1066 through 1074 or (resid 1075 and (name \ N or name CA or name C or name O or name CB )) or resid 1076 or (resid 1077 thr \ ough 1078 and (name N or name CA or name C or name O or name CB )) or resid 1079 \ through 1095 or (resid 1096 and (name N or name CA or name C or name O or name \ CB )) or resid 1097 through 1105 or (resid 1106 through 1107 and (name N or name \ CA or name C or name O or name CB )) or resid 1108 through 1119 or (resid 1120 \ through 1122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 123 through 1137 or resid 1301)) } ncs_group { reference = (chain 'E' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 117)) selection = (chain 'G' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 45 or (resid 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 63 or (re \ sid 64 and (name N or name CA or name C or name O or name CB )) or resid 65 thro \ ugh 117)) selection = (chain 'M' and (resid 2 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 117)) } ncs_group { reference = (chain 'H' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 107)) selection = (chain 'J' and (resid 1 through 68 or (resid 69 and (name N or name CA or name C \ or name O or name CB )) or resid 70 through 107)) selection = (chain 'P' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB )) or resid 6 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 68 or (resid 69 and (name \ N or name CA or name C or name O or name CB )) or resid 70 through 107)) } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 2.000 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: 1.330 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 73.050 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 : 0.014 0.379 32076 Z= 0.997 Angle : 1.983 45.816 43722 Z= 1.429 Chirality : 0.141 1.443 4921 Planarity : 0.007 0.120 5687 Dihedral : 13.356 121.674 11138 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.54 % Favored : 93.80 % Rotamer: Outliers : 1.16 % Allowed : 12.35 % Favored : 86.48 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4094 helix: 1.61 (0.19), residues: 583 sheet: 0.10 (0.15), residues: 1189 loop : -0.86 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP N 103 HIS 0.013 0.003 HIS B1064 PHE 0.037 0.003 PHE C1121 TYR 0.045 0.003 TYR C 265 ARG 0.008 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.02000 ( 3) link_NAG-ASN : angle 4.61122 ( 9) hydrogen bonds : bond 0.24880 ( 1061) hydrogen bonds : angle 9.53676 ( 2865) SS BOND : bond 0.10751 ( 44) SS BOND : angle 10.19090 ( 88) covalent geometry : bond 0.01317 (32029) covalent geometry : angle 1.93102 (43625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 3.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 GLN cc_start: 0.6187 (tm-30) cc_final: 0.5957 (tm-30) REVERT: B 740 MET cc_start: 0.7281 (ttt) cc_final: 0.7048 (ttt) REVERT: C 675 GLN cc_start: 0.6072 (tm130) cc_final: 0.5852 (tp40) REVERT: C 869 MET cc_start: 0.8091 (mtt) cc_final: 0.7800 (mtt) REVERT: N 105 TRP cc_start: 0.1065 (OUTLIER) cc_final: -0.0193 (t60) REVERT: H 4 MET cc_start: 0.0169 (mtp) cc_final: -0.0200 (tmt) REVERT: M 32 MET cc_start: -0.0406 (mmm) cc_final: -0.0739 (tmm) outliers start: 38 outliers final: 10 residues processed: 362 average time/residue: 1.0632 time to fit residues: 476.4149 Evaluate side-chains 216 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain N residue 105 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 50.0000 chunk 310 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 372 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 405 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 616 ASN A 709 ASN A 955 ASN A 965 GLN A1058 HIS A1135 ASN B 321 GLN B 405 ASN B 439 ASN B 532 ASN B 544 ASN B 606 ASN B 613 GLN B 762 GLN B 804 GLN B1074 ASN B1113 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 779 GLN C 895 GLN C1108 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN J 92 HIS N 33 HIS N 35 HIS ** N 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN G 54 ASN H 92 HIS ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 38 GLN M 54 ASN P 92 HIS Q 33 HIS Q 35 HIS ** Q 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.265579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.217064 restraints weight = 44667.291| |-----------------------------------------------------------------------------| r_work (start): 0.4536 rms_B_bonded: 2.67 r_work: 0.3995 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32076 Z= 0.204 Angle : 0.722 9.273 43722 Z= 0.392 Chirality : 0.049 0.285 4921 Planarity : 0.005 0.060 5687 Dihedral : 6.107 68.706 4556 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.96 % Favored : 95.02 % Rotamer: Outliers : 3.00 % Allowed : 13.73 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4094 helix: 0.93 (0.20), residues: 619 sheet: -0.22 (0.15), residues: 1219 loop : -1.04 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 353 HIS 0.015 0.002 HIS N 104 PHE 0.034 0.002 PHE B 541 TYR 0.028 0.002 TYR C 265 ARG 0.007 0.001 ARG C 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 3) link_NAG-ASN : angle 4.35210 ( 9) hydrogen bonds : bond 0.05472 ( 1061) hydrogen bonds : angle 6.81811 ( 2865) SS BOND : bond 0.00626 ( 44) SS BOND : angle 1.32803 ( 88) covalent geometry : bond 0.00456 (32029) covalent geometry : angle 0.71780 (43625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 225 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7900 (p) REVERT: A 675 GLN cc_start: 0.6755 (tm-30) cc_final: 0.6411 (tm-30) REVERT: B 206 LYS cc_start: 0.7968 (tptt) cc_final: 0.7602 (tppt) REVERT: B 702 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: B 1128 VAL cc_start: 0.6829 (m) cc_final: 0.6560 (t) REVERT: N 105 TRP cc_start: 0.1847 (OUTLIER) cc_final: 0.0056 (t60) REVERT: M 32 MET cc_start: -0.0163 (mmm) cc_final: -0.0599 (tmm) REVERT: P 4 MET cc_start: 0.2360 (tpt) cc_final: 0.1187 (ttp) outliers start: 98 outliers final: 40 residues processed: 300 average time/residue: 0.9744 time to fit residues: 370.4655 Evaluate side-chains 220 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain N residue 105 TRP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain R residue 28 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 221 optimal weight: 40.0000 chunk 254 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 344 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 266 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 227 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 439 ASN A 564 GLN A 901 GLN B 762 GLN B 978 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 439 ASN C1108 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.264943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.214619 restraints weight = 44905.857| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 2.74 r_work: 0.3873 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 32076 Z= 0.136 Angle : 0.618 11.068 43722 Z= 0.327 Chirality : 0.045 0.204 4921 Planarity : 0.005 0.051 5687 Dihedral : 5.398 56.702 4551 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.08 % Favored : 94.89 % Rotamer: Outliers : 3.00 % Allowed : 15.42 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4094 helix: 1.36 (0.21), residues: 594 sheet: -0.26 (0.15), residues: 1224 loop : -1.02 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.008 0.001 HIS A 207 PHE 0.028 0.002 PHE C 541 TYR 0.024 0.001 TYR C 265 ARG 0.006 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 3) link_NAG-ASN : angle 2.79917 ( 9) hydrogen bonds : bond 0.04273 ( 1061) hydrogen bonds : angle 6.12690 ( 2865) SS BOND : bond 0.00471 ( 44) SS BOND : angle 1.36848 ( 88) covalent geometry : bond 0.00306 (32029) covalent geometry : angle 0.61449 (43625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 194 time to evaluate : 3.508 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 553 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7893 (p) REVERT: A 675 GLN cc_start: 0.6605 (tm-30) cc_final: 0.6265 (tm-30) REVERT: A 740 MET cc_start: 0.8028 (ttt) cc_final: 0.7761 (ttm) REVERT: A 753 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7279 (tt) REVERT: B 170 TYR cc_start: 0.6858 (t80) cc_final: 0.6604 (t80) REVERT: B 564 GLN cc_start: 0.7701 (mt0) cc_final: 0.7407 (mt0) REVERT: B 1038 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7249 (mmtt) REVERT: B 1128 VAL cc_start: 0.7031 (m) cc_final: 0.6803 (t) REVERT: C 909 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6484 (pp) REVERT: G 32 MET cc_start: 0.1305 (mmt) cc_final: 0.0250 (ptm) REVERT: H 76 SER cc_start: 0.2090 (OUTLIER) cc_final: 0.1867 (t) REVERT: M 32 MET cc_start: -0.0668 (mmm) cc_final: -0.1117 (tmm) outliers start: 98 outliers final: 45 residues processed: 274 average time/residue: 0.9381 time to fit residues: 333.2879 Evaluate side-chains 219 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain N residue 105 TRP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 314 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 406 optimal weight: 40.0000 chunk 215 optimal weight: 30.0000 chunk 172 optimal weight: 5.9990 chunk 305 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 374 optimal weight: 50.0000 chunk 402 optimal weight: 50.0000 chunk 195 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 901 GLN B 762 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 965 GLN C1101 HIS ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.259647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.212283 restraints weight = 44908.736| |-----------------------------------------------------------------------------| r_work (start): 0.4512 rms_B_bonded: 2.92 r_work: 0.4174 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.4070 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 32076 Z= 0.305 Angle : 0.746 12.344 43722 Z= 0.396 Chirality : 0.051 0.243 4921 Planarity : 0.006 0.063 5687 Dihedral : 5.787 56.273 4545 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 3.92 % Allowed : 16.15 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4094 helix: 0.15 (0.20), residues: 616 sheet: -0.52 (0.15), residues: 1208 loop : -1.24 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 35 HIS 0.011 0.002 HIS C1048 PHE 0.030 0.003 PHE C1121 TYR 0.029 0.002 TYR C 265 ARG 0.010 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 3) link_NAG-ASN : angle 2.48253 ( 9) hydrogen bonds : bond 0.05469 ( 1061) hydrogen bonds : angle 6.38793 ( 2865) SS BOND : bond 0.00727 ( 44) SS BOND : angle 1.61494 ( 88) covalent geometry : bond 0.00724 (32029) covalent geometry : angle 0.74235 (43625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 182 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 675 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6588 (tm-30) REVERT: A 753 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 1038 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7240 (mttm) REVERT: A 1114 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7896 (tp) REVERT: B 546 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 564 GLN cc_start: 0.7799 (mt0) cc_final: 0.7549 (mt0) REVERT: B 974 SER cc_start: 0.8257 (t) cc_final: 0.7983 (p) REVERT: B 1038 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7427 (mmtt) REVERT: B 1111 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: B 1128 VAL cc_start: 0.6788 (m) cc_final: 0.6564 (t) REVERT: C 577 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7528 (ptp-110) REVERT: C 645 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.8008 (t) REVERT: C 675 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.5637 (tm130) REVERT: C 909 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6424 (pp) REVERT: M 32 MET cc_start: -0.0742 (mmm) cc_final: -0.1054 (tmm) outliers start: 128 outliers final: 71 residues processed: 288 average time/residue: 0.8770 time to fit residues: 326.8496 Evaluate side-chains 245 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1057 PRO Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 577 ARG Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 311 optimal weight: 50.0000 chunk 373 optimal weight: 40.0000 chunk 38 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 271 GLN B 762 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 965 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.261185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.212988 restraints weight = 44885.457| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 2.80 r_work: 0.4098 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32076 Z= 0.149 Angle : 0.611 10.385 43722 Z= 0.319 Chirality : 0.045 0.171 4921 Planarity : 0.005 0.057 5687 Dihedral : 5.259 56.738 4543 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 94.99 % Rotamer: Outliers : 3.19 % Allowed : 17.47 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4094 helix: 0.66 (0.21), residues: 622 sheet: -0.46 (0.15), residues: 1224 loop : -1.21 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 105 HIS 0.006 0.001 HIS I 104 PHE 0.019 0.001 PHE C1121 TYR 0.028 0.001 TYR C 265 ARG 0.008 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 3) link_NAG-ASN : angle 1.95603 ( 9) hydrogen bonds : bond 0.04186 ( 1061) hydrogen bonds : angle 5.88376 ( 2865) SS BOND : bond 0.00399 ( 44) SS BOND : angle 1.32471 ( 88) covalent geometry : bond 0.00343 (32029) covalent geometry : angle 0.60767 (43625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 174 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8504 (mp) REVERT: A 675 GLN cc_start: 0.6703 (tm-30) cc_final: 0.6374 (tm-30) REVERT: A 1038 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7099 (mttm) REVERT: B 546 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7808 (mm) REVERT: B 564 GLN cc_start: 0.7653 (mt0) cc_final: 0.7452 (mt0) REVERT: B 586 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: B 740 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8022 (ttt) REVERT: B 974 SER cc_start: 0.8378 (t) cc_final: 0.8028 (p) REVERT: B 1038 LYS cc_start: 0.7400 (mmtt) cc_final: 0.7129 (mmtt) REVERT: B 1128 VAL cc_start: 0.6792 (m) cc_final: 0.6582 (t) REVERT: C 740 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7817 (ttt) REVERT: C 909 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6290 (pp) REVERT: G 32 MET cc_start: 0.1033 (mmt) cc_final: 0.0286 (ptm) REVERT: G 112 MET cc_start: 0.3200 (mmm) cc_final: 0.2677 (mmt) REVERT: M 32 MET cc_start: -0.0616 (mmm) cc_final: -0.1117 (tmm) REVERT: P 4 MET cc_start: 0.2154 (tpt) cc_final: 0.1258 (ttt) outliers start: 104 outliers final: 55 residues processed: 256 average time/residue: 0.9684 time to fit residues: 317.4796 Evaluate side-chains 225 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 163 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 213 optimal weight: 40.0000 chunk 245 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 328 optimal weight: 8.9990 chunk 350 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 872 GLN B 978 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 955 ASN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.260508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.211754 restraints weight = 44937.977| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 2.94 r_work: 0.3859 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32076 Z= 0.202 Angle : 0.642 13.500 43722 Z= 0.334 Chirality : 0.046 0.195 4921 Planarity : 0.005 0.064 5687 Dihedral : 5.282 58.482 4543 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.72 % Favored : 94.26 % Rotamer: Outliers : 3.59 % Allowed : 17.59 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 4094 helix: 0.63 (0.21), residues: 606 sheet: -0.50 (0.14), residues: 1271 loop : -1.24 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 105 HIS 0.011 0.001 HIS A 207 PHE 0.024 0.002 PHE C1121 TYR 0.030 0.002 TYR C 265 ARG 0.005 0.000 ARG C 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 3) link_NAG-ASN : angle 1.94372 ( 9) hydrogen bonds : bond 0.04469 ( 1061) hydrogen bonds : angle 5.88825 ( 2865) SS BOND : bond 0.00500 ( 44) SS BOND : angle 1.40063 ( 88) covalent geometry : bond 0.00473 (32029) covalent geometry : angle 0.63891 (43625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 169 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 675 GLN cc_start: 0.6782 (tm-30) cc_final: 0.6349 (tm-30) REVERT: A 1038 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7130 (mttm) REVERT: B 546 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7857 (mm) REVERT: B 564 GLN cc_start: 0.7861 (mt0) cc_final: 0.7648 (mt0) REVERT: B 702 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: B 740 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7849 (ttt) REVERT: B 974 SER cc_start: 0.8512 (t) cc_final: 0.8045 (p) REVERT: B 1038 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7532 (mmtt) REVERT: B 1111 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: C 326 ILE cc_start: 0.7488 (pt) cc_final: 0.7253 (pp) REVERT: C 461 LEU cc_start: -0.1358 (OUTLIER) cc_final: -0.1704 (mm) REVERT: C 740 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: C 909 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6363 (pp) REVERT: G 32 MET cc_start: 0.1316 (mmt) cc_final: 0.0534 (ptm) REVERT: M 32 MET cc_start: -0.0698 (mmm) cc_final: -0.1244 (tmm) outliers start: 117 outliers final: 73 residues processed: 262 average time/residue: 0.8696 time to fit residues: 296.8822 Evaluate side-chains 242 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 160 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1111 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 127 optimal weight: 0.0470 chunk 319 optimal weight: 10.0000 chunk 193 optimal weight: 0.2980 chunk 26 optimal weight: 30.0000 chunk 374 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 327 optimal weight: 5.9990 chunk 36 optimal weight: 30.0000 chunk 401 optimal weight: 50.0000 chunk 294 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 872 GLN B 978 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.261370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.214226 restraints weight = 44946.032| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 2.80 r_work: 0.4152 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32076 Z= 0.133 Angle : 0.584 14.817 43722 Z= 0.301 Chirality : 0.044 0.160 4921 Planarity : 0.004 0.060 5687 Dihedral : 4.936 58.726 4543 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 2.91 % Allowed : 18.76 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4094 helix: 1.06 (0.21), residues: 607 sheet: -0.44 (0.14), residues: 1253 loop : -1.12 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 36 HIS 0.007 0.001 HIS A 207 PHE 0.021 0.001 PHE C 65 TYR 0.024 0.001 TYR C 265 ARG 0.003 0.000 ARG N 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 1.59431 ( 9) hydrogen bonds : bond 0.03809 ( 1061) hydrogen bonds : angle 5.58044 ( 2865) SS BOND : bond 0.00335 ( 44) SS BOND : angle 1.18796 ( 88) covalent geometry : bond 0.00308 (32029) covalent geometry : angle 0.58182 (43625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8188 Ramachandran restraints generated. 4094 Oldfield, 0 Emsley, 4094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 179 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 GLN cc_start: 0.6646 (tm-30) cc_final: 0.6284 (tm-30) REVERT: A 761 THR cc_start: 0.8402 (m) cc_final: 0.8109 (m) REVERT: A 1038 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6714 (mttm) REVERT: B 226 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7752 (pp) REVERT: B 489 TYR cc_start: 0.3026 (OUTLIER) cc_final: 0.2800 (p90) REVERT: B 702 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 974 SER cc_start: 0.8359 (t) cc_final: 0.8001 (p) REVERT: B 1038 LYS cc_start: 0.7454 (mmtt) cc_final: 0.7203 (mmtt) REVERT: C 909 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6475 (pp) REVERT: G 32 MET cc_start: 0.1247 (mmt) cc_final: 0.0435 (ptm) REVERT: G 112 MET cc_start: 0.3011 (mmm) cc_final: 0.2443 (mmt) REVERT: H 4 MET cc_start: 0.2598 (ppp) cc_final: 0.2186 (pp-130) REVERT: H 106 ILE cc_start: 0.1935 (OUTLIER) cc_final: 0.1453 (pt) REVERT: M 20 LEU cc_start: -0.2110 (OUTLIER) cc_final: -0.2440 (pp) REVERT: M 32 MET cc_start: -0.0865 (mmm) cc_final: -0.1231 (tmm) REVERT: Q 83 MET cc_start: 0.0036 (mmp) cc_final: -0.0529 (mmp) outliers start: 95 outliers final: 59 residues processed: 252 average time/residue: 0.9205 time to fit residues: 299.6049 Evaluate side-chains 231 residues out of total 3608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 112 MET Chi-restraints excluded: chain P residue 5 THR Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9606 > 50: distance: 13 - 18: 7.508 distance: 18 - 19: 10.250 distance: 18 - 162: 7.633 distance: 19 - 20: 3.858 distance: 19 - 22: 4.921 distance: 20 - 21: 5.910 distance: 21 - 159: 8.826 distance: 22 - 23: 9.186 distance: 24 - 25: 8.457 distance: 25 - 28: 4.899 distance: 26 - 27: 6.330 distance: 26 - 32: 5.792 distance: 28 - 29: 8.168 distance: 29 - 30: 5.606 distance: 29 - 31: 11.160 distance: 32 - 33: 10.972 distance: 32 - 154: 4.609 distance: 33 - 36: 17.276 distance: 34 - 35: 9.750 distance: 34 - 43: 3.547 distance: 35 - 151: 7.368 distance: 36 - 37: 5.662 distance: 37 - 38: 4.840 distance: 37 - 39: 5.151 distance: 38 - 40: 20.162 distance: 39 - 41: 8.187 distance: 40 - 42: 6.230 distance: 41 - 42: 9.816 distance: 43 - 44: 14.264 distance: 44 - 45: 4.326 distance: 44 - 47: 12.188 distance: 47 - 48: 8.845 distance: 48 - 49: 10.107 distance: 49 - 50: 4.265 distance: 50 - 51: 6.821 distance: 51 - 52: 7.466 distance: 51 - 53: 6.165 distance: 54 - 55: 6.251 distance: 55 - 56: 4.405 distance: 55 - 58: 7.386 distance: 56 - 57: 11.513 distance: 56 - 61: 10.742 distance: 58 - 59: 16.625 distance: 58 - 60: 11.126 distance: 61 - 62: 13.760 distance: 62 - 63: 13.303 distance: 62 - 65: 20.630 distance: 63 - 64: 17.269 distance: 63 - 70: 9.575 distance: 65 - 66: 32.052 distance: 66 - 67: 33.216 distance: 67 - 68: 13.594 distance: 67 - 69: 8.060 distance: 70 - 71: 10.322 distance: 70 - 76: 25.658 distance: 71 - 72: 7.503 distance: 71 - 74: 29.230 distance: 72 - 73: 32.574 distance: 72 - 77: 8.107 distance: 74 - 75: 28.417 distance: 75 - 76: 7.553 distance: 77 - 78: 13.386 distance: 78 - 79: 9.660 distance: 78 - 81: 10.800 distance: 79 - 80: 15.175 distance: 79 - 84: 6.341 distance: 81 - 82: 4.320 distance: 81 - 83: 9.640 distance: 84 - 85: 3.809 distance: 85 - 86: 8.351 distance: 85 - 88: 7.726 distance: 86 - 87: 7.154 distance: 86 - 93: 10.152 distance: 88 - 89: 7.028 distance: 89 - 90: 4.394 distance: 90 - 91: 7.818 distance: 90 - 92: 7.848 distance: 93 - 94: 6.697 distance: 94 - 95: 4.239 distance: 94 - 97: 4.059 distance: 97 - 98: 9.548