Starting phenix.real_space_refine on Fri Mar 6 16:29:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e3k_30982/03_2026/7e3k_30982.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 134 5.16 5 C 20629 2.51 5 N 5455 2.21 5 O 6321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7591 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 9, 'ASN:plan1': 3, 'GLN:plan1': 6, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 7571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7571 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 9, 'ASN:plan1': 3, 'GLN:plan1': 6, 'PHE:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7577 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 8 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 9, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1570 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 209} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1594 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 202} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 8.14, per 1000 atoms: 0.25 Number of scatterers: 32539 At special positions: 0 Unit cell: (137.76, 136.94, 262.4, 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 134 16.00 O 6321 8.00 N 5455 7.00 C 20629 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.04 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM32285 O5 NAG A1304 .*. O " rejected from bonding due to valence issues. Atom "HETATM32355 O5 NAG B1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM32369 O5 NAG B1302 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7980 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 19.5% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.930A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.603A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.400A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.879A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.076A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.305A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.300A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.250A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.897A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.603A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.400A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.881A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.077A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.590A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.686A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.306A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.249A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.930A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.399A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.880A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.076A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.589A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.685A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.306A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.249A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 removed outlier: 4.092A pdb=" N GLY D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 200' Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.603A pdb=" N LEU E 126 " --> pdb=" O SER E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.848A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 200 removed outlier: 4.093A pdb=" N GLY F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 196 through 200' Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 122 through 129 removed outlier: 3.602A pdb=" N LEU G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.849A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 200 removed outlier: 4.093A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 200' Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.602A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.248A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.665A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.826A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.498A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.665A 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: 3.647A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.401A 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 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB9, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.249A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.237A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.664A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.825A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.505A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.646A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.652A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.765A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.765A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.671A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.858A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.248A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.665A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.825A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.197A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.645A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.647A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.653A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.764A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.673A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.594A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 92 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU D 10 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 92 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 160 through 164 removed outlier: 4.034A pdb=" N CYS D 206 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 219 " --> pdb=" O CYS D 206 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.538A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 64 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.760A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER E 132 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU E 182 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL E 134 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU E 180 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU E 136 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER E 178 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASN E 138 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU E 176 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.518A pdb=" N TYR E 193 " --> pdb=" O PHE E 210 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.593A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU F 10 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 92 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLU F 10 " --> pdb=" O MET F 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 92 " --> pdb=" O VAL F 119 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 160 through 164 removed outlier: 4.034A pdb=" N CYS F 206 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 219 " --> pdb=" O CYS F 206 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.539A pdb=" N THR G 5 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 64 " --> pdb=" O THR G 75 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.762A pdb=" N SER G 115 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN G 138 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER G 132 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU G 182 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL G 134 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU G 180 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU G 136 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER G 178 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN G 138 " --> pdb=" O LEU G 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU G 176 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 146 through 148 removed outlier: 3.517A pdb=" N TYR G 193 " --> pdb=" O PHE G 210 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AH9, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.594A pdb=" N ALA H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.511A pdb=" N GLU H 10 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 145 through 155 removed outlier: 5.596A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 160 through 164 removed outlier: 4.035A pdb=" N CYS H 206 " --> pdb=" O LYS H 219 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS H 219 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.539A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.823A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.761A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 146 through 148 removed outlier: 3.517A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 150 through 151 1228 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.87 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8938 1.33 - 1.45: 6751 1.45 - 1.58: 17398 1.58 - 1.70: 0 1.70 - 1.82: 169 Bond restraints: 33256 Sorted by residual: bond pdb=" N LYS G 108 " pdb=" CA LYS G 108 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.45e+01 bond pdb=" N LYS E 108 " pdb=" CA LYS E 108 " ideal model delta sigma weight residual 1.457 1.488 -0.032 6.40e-03 2.44e+04 2.42e+01 bond pdb=" N LYS L 108 " pdb=" CA LYS L 108 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.39e+01 bond pdb=" C ASP C 808 " pdb=" N PRO C 809 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" N CYS A 617 " pdb=" CA CYS A 617 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 33251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 43955 2.49 - 4.97: 1264 4.97 - 7.46: 109 7.46 - 9.94: 8 9.94 - 12.43: 1 Bond angle restraints: 45337 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.23 104.03 9.20 1.24e+00 6.50e-01 5.50e+01 angle pdb=" N THR A 618 " pdb=" CA THR A 618 " pdb=" C THR A 618 " ideal model delta sigma weight residual 113.97 105.15 8.82 1.28e+00 6.10e-01 4.75e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.72 104.95 8.77 1.30e+00 5.92e-01 4.55e+01 angle pdb=" N THR C 602 " pdb=" CA THR C 602 " pdb=" C THR C 602 " ideal model delta sigma weight residual 111.28 103.95 7.33 1.09e+00 8.42e-01 4.52e+01 angle pdb=" CA ASP A 138 " pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 117.43 122.94 -5.51 8.50e-01 1.38e+00 4.20e+01 ... (remaining 45332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.87: 18813 20.87 - 41.73: 1064 41.73 - 62.60: 112 62.60 - 83.46: 38 83.46 - 104.33: 20 Dihedral angle restraints: 20047 sinusoidal: 7642 harmonic: 12405 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.26 -86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.26 -86.26 1 1.00e+01 1.00e-02 8.97e+01 ... (remaining 20044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 5246 0.264 - 0.527: 11 0.527 - 0.791: 1 0.791 - 1.054: 6 1.054 - 1.318: 1 Chirality restraints: 5265 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.08 -1.32 2.00e-01 2.50e+01 4.34e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 5262 not shown) Planarity restraints: 5879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.297 2.00e-02 2.50e+03 2.55e-01 8.12e+02 pdb=" C7 NAG A1301 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.170 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.284 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" C7 NAG A1305 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.162 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.431 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " 0.203 2.00e-02 2.50e+03 2.15e-01 5.75e+02 pdb=" CG ASN A 234 " -0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.149 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " -0.264 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.299 2.00e-02 2.50e+03 ... (remaining 5876 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 320 2.59 - 3.17: 28431 3.17 - 3.74: 46057 3.74 - 4.32: 63647 4.32 - 4.90: 107094 Nonbonded interactions: 245549 Sorted by model distance: nonbonded pdb=" OD1 ASN A 234 " pdb=" C1 NAG A1304 " model vdw 2.011 2.776 nonbonded pdb=" O ASN B 616 " pdb=" OD1 ASN B 616 " model vdw 2.065 3.040 nonbonded pdb=" O PRO A1053 " pdb=" NE2 GLN A1054 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASN A 196 " pdb=" N ILE A 197 " model vdw 2.241 3.120 nonbonded pdb=" O PRO C1053 " pdb=" NE2 GLN C1054 " model vdw 2.242 3.120 ... (remaining 245544 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 132 or (resid 133 through 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 197 \ or (resid 198 and (name N or name CA or name C or name O or name CB )) or resid \ 199 through 200 or (resid 201 and (name N or name CA or name C or name O or nam \ e CB )) or resid 202 through 739 or (resid 740 and (name N or name CA or name C \ or name O or name CB )) or resid 741 through 810 or (resid 811 and (name N or na \ me CA or name C or name O or name CB )) or resid 812 through 982 or (resid 983 a \ nd (name N or name CA or name C or name O or name CB )) or resid 984 through 130 \ 6)) selection = (chain 'B' and (resid 27 through 132 or (resid 133 through 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 197 or (resid 198 a \ nd (name N or name CA or name C or name O or name CB )) or resid 199 through 226 \ or (resid 227 and (name N or name CA or name C or name O or name CB )) or resid \ 228 through 1306)) selection = (chain 'C' and (resid 27 through 739 or (resid 740 and (name N or name CA or nam \ e C or name O or name CB )) or resid 741 through 778 or (resid 779 and (name N o \ r name CA or name C or name O or name CB )) or resid 780 through 810 or (resid 8 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 812 through \ 982 or (resid 983 and (name N or name CA or name C or name O or name CB )) or r \ esid 984 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 35.160 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.537 33325 Z= 0.457 Angle : 1.138 46.494 45497 Z= 0.619 Chirality : 0.069 1.318 5265 Planarity : 0.008 0.255 5857 Dihedral : 12.980 104.329 11926 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.98 % Rotamer: Outliers : 0.12 % Allowed : 1.43 % Favored : 98.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 4212 helix: 0.79 (0.20), residues: 720 sheet: -1.38 (0.14), residues: 1240 loop : -1.92 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 983 TYR 0.026 0.002 TYR L 187 PHE 0.043 0.002 PHE C 92 TRP 0.015 0.002 TRP F 50 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00784 (33256) covalent geometry : angle 0.94365 (45337) SS BOND : bond 0.00622 ( 47) SS BOND : angle 2.98150 ( 94) hydrogen bonds : bond 0.22477 ( 1165) hydrogen bonds : angle 8.92517 ( 3300) link_NAG-ASN : bond 0.13616 ( 22) link_NAG-ASN : angle 16.38736 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 TYR cc_start: 0.5185 (m-10) cc_final: 0.4706 (m-80) REVERT: G 184 LYS cc_start: 0.4932 (tptt) cc_final: 0.4185 (tptt) REVERT: G 188 GLU cc_start: 0.5590 (mp0) cc_final: 0.4435 (tp30) outliers start: 4 outliers final: 1 residues processed: 233 average time/residue: 0.2608 time to fit residues: 88.4539 Evaluate side-chains 124 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 815 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 50.0000 chunk 155 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 955 ASN B 690 GLN B 762 GLN B 784 GLN B 955 ASN C 955 ASN E 43 GLN G 190 HIS H 43 GLN L 38 GLN L 43 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.066027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040690 restraints weight = 292874.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040795 restraints weight = 157365.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.041013 restraints weight = 104532.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041144 restraints weight = 77696.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.041211 restraints weight = 70343.442| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33325 Z= 0.169 Angle : 0.662 9.154 45497 Z= 0.347 Chirality : 0.046 0.176 5265 Planarity : 0.005 0.080 5857 Dihedral : 6.040 59.669 5031 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 0.67 % Allowed : 6.80 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4212 helix: 1.48 (0.20), residues: 712 sheet: -1.06 (0.14), residues: 1276 loop : -1.36 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 30 TYR 0.025 0.001 TYR H 80 PHE 0.029 0.001 PHE L 72 TRP 0.012 0.001 TRP D 36 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00365 (33256) covalent geometry : angle 0.65000 (45337) SS BOND : bond 0.00527 ( 47) SS BOND : angle 1.14439 ( 94) hydrogen bonds : bond 0.05197 ( 1165) hydrogen bonds : angle 6.22540 ( 3300) link_NAG-ASN : bond 0.00685 ( 22) link_NAG-ASN : angle 3.16775 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 83 ASP cc_start: 0.6003 (m-30) cc_final: 0.5803 (m-30) REVERT: G 80 GLU cc_start: 0.7487 (pt0) cc_final: 0.7147 (pp20) REVERT: G 184 LYS cc_start: 0.8445 (tptt) cc_final: 0.8217 (tptt) REVERT: L 62 ARG cc_start: 0.5838 (mtm-85) cc_final: 0.5240 (ptt-90) outliers start: 23 outliers final: 11 residues processed: 164 average time/residue: 0.2741 time to fit residues: 65.0650 Evaluate side-chains 126 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 279 optimal weight: 0.5980 chunk 324 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 chunk 252 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 377 optimal weight: 40.0000 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 644 GLN B1106 GLN C1106 GLN D 181 GLN E 43 GLN H 43 GLN L 43 GLN L 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.064232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039166 restraints weight = 293614.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038886 restraints weight = 163757.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.039344 restraints weight = 109497.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.039437 restraints weight = 77485.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.039507 restraints weight = 71182.118| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33325 Z= 0.199 Angle : 0.634 7.875 45497 Z= 0.330 Chirality : 0.044 0.184 5265 Planarity : 0.005 0.078 5857 Dihedral : 5.502 59.893 5027 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.02 % Allowed : 9.28 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4212 helix: 1.78 (0.20), residues: 701 sheet: -0.98 (0.14), residues: 1302 loop : -1.24 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 62 TYR 0.018 0.001 TYR H 95 PHE 0.027 0.001 PHE L 84 TRP 0.011 0.001 TRP G 36 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00437 (33256) covalent geometry : angle 0.62464 (45337) SS BOND : bond 0.00353 ( 47) SS BOND : angle 1.26742 ( 94) hydrogen bonds : bond 0.04753 ( 1165) hydrogen bonds : angle 5.72268 ( 3300) link_NAG-ASN : bond 0.00295 ( 22) link_NAG-ASN : angle 2.56371 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8874 (mmm) cc_final: 0.8617 (mpp) REVERT: B 902 MET cc_start: 0.9413 (tpp) cc_final: 0.9205 (tpt) REVERT: C 1050 MET cc_start: 0.8795 (ptp) cc_final: 0.8207 (ptp) REVERT: F 220 LYS cc_start: 0.7131 (tptt) cc_final: 0.6927 (mmtm) REVERT: G 18 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7831 (ttm-80) REVERT: G 146 LYS cc_start: 0.8157 (tttt) cc_final: 0.7840 (mtmm) REVERT: L 17 GLU cc_start: 0.6178 (mp0) cc_final: 0.5778 (mp0) REVERT: L 18 ARG cc_start: 0.7806 (tmm160) cc_final: 0.7561 (tmm160) REVERT: L 170 LYS cc_start: 0.5858 (pptt) cc_final: 0.5583 (pptt) REVERT: L 212 ARG cc_start: 0.7962 (mtp85) cc_final: 0.6802 (mmp-170) outliers start: 35 outliers final: 17 residues processed: 154 average time/residue: 0.2664 time to fit residues: 60.6097 Evaluate side-chains 123 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 173 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 364 optimal weight: 50.0000 chunk 175 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 295 optimal weight: 0.3980 chunk 224 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 289 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1106 GLN E 43 GLN H 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.065074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.040461 restraints weight = 291153.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.039989 restraints weight = 163409.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040367 restraints weight = 107157.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.040542 restraints weight = 80027.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040623 restraints weight = 70969.600| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33325 Z= 0.101 Angle : 0.543 7.438 45497 Z= 0.283 Chirality : 0.043 0.213 5265 Planarity : 0.004 0.078 5857 Dihedral : 5.085 59.671 5027 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.11 % Allowed : 10.09 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4212 helix: 2.18 (0.20), residues: 703 sheet: -0.77 (0.14), residues: 1287 loop : -1.05 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 107 TYR 0.019 0.001 TYR D 80 PHE 0.008 0.001 PHE C 238 TRP 0.019 0.001 TRP D 36 HIS 0.002 0.000 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00213 (33256) covalent geometry : angle 0.53482 (45337) SS BOND : bond 0.00415 ( 47) SS BOND : angle 1.06734 ( 94) hydrogen bonds : bond 0.04000 ( 1165) hydrogen bonds : angle 5.25712 ( 3300) link_NAG-ASN : bond 0.00317 ( 22) link_NAG-ASN : angle 2.20283 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.9073 (p0) REVERT: C 1050 MET cc_start: 0.8633 (ptp) cc_final: 0.8163 (ptp) REVERT: L 124 GLU cc_start: 0.5626 (pm20) cc_final: 0.5383 (pm20) REVERT: L 139 ASN cc_start: 0.7126 (p0) cc_final: 0.6854 (t0) outliers start: 38 outliers final: 17 residues processed: 146 average time/residue: 0.2641 time to fit residues: 56.8350 Evaluate side-chains 125 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 43 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 106 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 133 optimal weight: 9.9990 chunk 314 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 287 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 369 optimal weight: 50.0000 chunk 57 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN A1101 HIS A1106 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1101 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.062388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037187 restraints weight = 297017.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036814 restraints weight = 171764.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.037015 restraints weight = 116855.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037170 restraints weight = 89948.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.037245 restraints weight = 77212.333| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 33325 Z= 0.389 Angle : 0.808 10.405 45497 Z= 0.413 Chirality : 0.046 0.195 5265 Planarity : 0.005 0.077 5857 Dihedral : 5.845 59.857 5027 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 1.87 % Allowed : 11.06 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4212 helix: 1.27 (0.19), residues: 710 sheet: -1.02 (0.14), residues: 1320 loop : -1.22 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 107 TYR 0.028 0.002 TYR D 80 PHE 0.032 0.002 PHE C 855 TRP 0.016 0.002 TRP C 886 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00843 (33256) covalent geometry : angle 0.80040 (45337) SS BOND : bond 0.00474 ( 47) SS BOND : angle 1.57669 ( 94) hydrogen bonds : bond 0.05515 ( 1165) hydrogen bonds : angle 5.95185 ( 3300) link_NAG-ASN : bond 0.00660 ( 22) link_NAG-ASN : angle 2.58993 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8929 (mmm) cc_final: 0.8624 (mpp) REVERT: D 74 MET cc_start: 0.8051 (mpp) cc_final: 0.7747 (mmm) REVERT: E 62 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5951 (ptm-80) REVERT: F 216 LYS cc_start: 0.7883 (mptt) cc_final: 0.7303 (tptt) REVERT: G 189 LYS cc_start: 0.7560 (pptt) cc_final: 0.7180 (pttp) REVERT: H 2 MET cc_start: 0.8697 (ttm) cc_final: 0.8459 (tpp) REVERT: L 139 ASN cc_start: 0.6722 (p0) cc_final: 0.6459 (t0) outliers start: 64 outliers final: 39 residues processed: 173 average time/residue: 0.2438 time to fit residues: 64.3070 Evaluate side-chains 148 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 CYS Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 184 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 216 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 414 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 297 optimal weight: 30.0000 chunk 266 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1106 GLN C 321 GLN E 43 GLN F 1 GLN H 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.063302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.038651 restraints weight = 292761.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038147 restraints weight = 165363.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038513 restraints weight = 112244.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.038845 restraints weight = 80502.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038758 restraints weight = 65886.824| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33325 Z= 0.163 Angle : 0.586 8.079 45497 Z= 0.305 Chirality : 0.044 0.195 5265 Planarity : 0.004 0.077 5857 Dihedral : 5.317 59.966 5027 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.28 % Allowed : 12.46 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4212 helix: 1.88 (0.20), residues: 718 sheet: -0.88 (0.14), residues: 1320 loop : -1.06 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 107 TYR 0.027 0.001 TYR D 80 PHE 0.016 0.001 PHE E 72 TRP 0.015 0.001 TRP D 36 HIS 0.003 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00360 (33256) covalent geometry : angle 0.57850 (45337) SS BOND : bond 0.00336 ( 47) SS BOND : angle 1.14670 ( 94) hydrogen bonds : bond 0.04401 ( 1165) hydrogen bonds : angle 5.40468 ( 3300) link_NAG-ASN : bond 0.00234 ( 22) link_NAG-ASN : angle 2.17651 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8809 (mmm) cc_final: 0.8539 (mpp) REVERT: B 1101 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7404 (m-70) REVERT: C 740 MET cc_start: 0.9181 (tpp) cc_final: 0.8661 (tpp) REVERT: D 74 MET cc_start: 0.8018 (mpp) cc_final: 0.7645 (mmm) REVERT: F 216 LYS cc_start: 0.7887 (mptt) cc_final: 0.7247 (tptt) REVERT: G 189 LYS cc_start: 0.7618 (pptt) cc_final: 0.7303 (pttt) REVERT: L 139 ASN cc_start: 0.6792 (p0) cc_final: 0.6546 (t0) outliers start: 44 outliers final: 31 residues processed: 149 average time/residue: 0.2561 time to fit residues: 57.3379 Evaluate side-chains 137 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain H residue 106 CYS Chi-restraints excluded: chain H residue 107 ARG Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 105 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 410 optimal weight: 0.0470 chunk 161 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 309 optimal weight: 0.4980 chunk 132 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN C 196 ASN C 334 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 43 GLN L 43 GLN L 211 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.064020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.039604 restraints weight = 290924.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.039002 restraints weight = 154929.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.039469 restraints weight = 105826.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.039731 restraints weight = 77256.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039838 restraints weight = 65674.403| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33325 Z= 0.104 Angle : 0.549 9.144 45497 Z= 0.286 Chirality : 0.043 0.200 5265 Planarity : 0.004 0.079 5857 Dihedral : 4.950 59.762 5027 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.37 % Allowed : 12.51 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4212 helix: 2.45 (0.20), residues: 694 sheet: -0.67 (0.14), residues: 1321 loop : -0.95 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 62 TYR 0.016 0.001 TYR B1067 PHE 0.012 0.001 PHE G 63 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00227 (33256) covalent geometry : angle 0.54300 (45337) SS BOND : bond 0.00304 ( 47) SS BOND : angle 1.00742 ( 94) hydrogen bonds : bond 0.03922 ( 1165) hydrogen bonds : angle 5.06921 ( 3300) link_NAG-ASN : bond 0.00272 ( 22) link_NAG-ASN : angle 1.98660 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8811 (mmm) cc_final: 0.8367 (mpp) REVERT: D 74 MET cc_start: 0.8111 (mpp) cc_final: 0.7823 (mmm) REVERT: D 81 MET cc_start: 0.6333 (mtp) cc_final: 0.6129 (mmm) REVERT: F 2 MET cc_start: 0.5788 (ttt) cc_final: 0.4946 (tmm) REVERT: F 216 LYS cc_start: 0.7909 (mptt) cc_final: 0.7292 (tptt) REVERT: G 189 LYS cc_start: 0.7591 (pptt) cc_final: 0.7288 (pttt) REVERT: L 139 ASN cc_start: 0.6746 (p0) cc_final: 0.6524 (t0) outliers start: 47 outliers final: 30 residues processed: 155 average time/residue: 0.2511 time to fit residues: 58.5136 Evaluate side-chains 137 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 184 LYS Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 107 optimal weight: 0.0030 chunk 194 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 340 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 chunk 418 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 overall best weight: 3.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN H 43 GLN L 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.063220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038741 restraints weight = 292839.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038183 restraints weight = 162726.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.038561 restraints weight = 109221.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.038670 restraints weight = 81702.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038809 restraints weight = 70997.475| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33325 Z= 0.178 Angle : 0.590 9.116 45497 Z= 0.305 Chirality : 0.043 0.183 5265 Planarity : 0.004 0.081 5857 Dihedral : 5.050 59.578 5027 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.66 % Allowed : 12.63 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4212 helix: 2.32 (0.20), residues: 700 sheet: -0.66 (0.14), residues: 1290 loop : -0.93 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 62 TYR 0.017 0.001 TYR B1067 PHE 0.018 0.001 PHE C 855 TRP 0.009 0.001 TRP H 164 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00395 (33256) covalent geometry : angle 0.58270 (45337) SS BOND : bond 0.00364 ( 47) SS BOND : angle 1.22554 ( 94) hydrogen bonds : bond 0.04149 ( 1165) hydrogen bonds : angle 5.16414 ( 3300) link_NAG-ASN : bond 0.00227 ( 22) link_NAG-ASN : angle 2.06315 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 110 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8855 (mmm) cc_final: 0.8492 (mpp) REVERT: C 1101 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7290 (m90) REVERT: D 74 MET cc_start: 0.8140 (mpp) cc_final: 0.7849 (mmm) REVERT: D 81 MET cc_start: 0.6180 (mtp) cc_final: 0.5937 (mmm) REVERT: F 2 MET cc_start: 0.5981 (ttt) cc_final: 0.5113 (tmm) REVERT: F 216 LYS cc_start: 0.7943 (mptt) cc_final: 0.7293 (tptt) REVERT: G 189 LYS cc_start: 0.7604 (pptt) cc_final: 0.7294 (pttt) REVERT: H 220 LYS cc_start: 0.5041 (pptt) cc_final: 0.4554 (mmmt) REVERT: L 139 ASN cc_start: 0.6712 (p0) cc_final: 0.6487 (t0) outliers start: 57 outliers final: 38 residues processed: 160 average time/residue: 0.2233 time to fit residues: 54.4248 Evaluate side-chains 145 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 407 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 359 optimal weight: 40.0000 chunk 275 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN H 43 GLN H 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.063160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.039025 restraints weight = 290790.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039288 restraints weight = 173829.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.039201 restraints weight = 115970.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039137 restraints weight = 82252.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039070 restraints weight = 78891.027| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33325 Z= 0.157 Angle : 0.583 12.215 45497 Z= 0.301 Chirality : 0.043 0.179 5265 Planarity : 0.004 0.083 5857 Dihedral : 5.055 59.895 5027 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.40 % Allowed : 12.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4212 helix: 2.31 (0.20), residues: 709 sheet: -0.62 (0.14), residues: 1274 loop : -0.95 (0.13), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.016 0.001 TYR B1067 PHE 0.014 0.001 PHE C 855 TRP 0.010 0.001 TRP H 164 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00349 (33256) covalent geometry : angle 0.57705 (45337) SS BOND : bond 0.00339 ( 47) SS BOND : angle 1.11475 ( 94) hydrogen bonds : bond 0.04078 ( 1165) hydrogen bonds : angle 5.09469 ( 3300) link_NAG-ASN : bond 0.00214 ( 22) link_NAG-ASN : angle 1.99433 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8851 (mmm) cc_final: 0.8432 (mpp) REVERT: C 1101 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7361 (m90) REVERT: D 74 MET cc_start: 0.8146 (mpp) cc_final: 0.7793 (mmm) REVERT: D 81 MET cc_start: 0.6912 (mtp) cc_final: 0.6609 (mmm) REVERT: F 2 MET cc_start: 0.5679 (ttt) cc_final: 0.4817 (tmm) REVERT: F 216 LYS cc_start: 0.7951 (mptt) cc_final: 0.7167 (tptt) REVERT: G 189 LYS cc_start: 0.7536 (pptt) cc_final: 0.7136 (pttt) REVERT: H 220 LYS cc_start: 0.5106 (pptt) cc_final: 0.4629 (mmmt) REVERT: L 139 ASN cc_start: 0.6581 (p0) cc_final: 0.6350 (t0) outliers start: 48 outliers final: 39 residues processed: 149 average time/residue: 0.2577 time to fit residues: 57.7922 Evaluate side-chains 145 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 184 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 27 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 383 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 416 optimal weight: 40.0000 chunk 317 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 99 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 43 GLN L 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.060292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038755 restraints weight = 295953.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038304 restraints weight = 166074.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.038575 restraints weight = 108469.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038748 restraints weight = 80717.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.038837 restraints weight = 66164.878| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 33325 Z= 0.255 Angle : 0.687 9.904 45497 Z= 0.352 Chirality : 0.044 0.276 5265 Planarity : 0.005 0.083 5857 Dihedral : 5.487 59.511 5027 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 1.31 % Allowed : 13.10 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4212 helix: 1.75 (0.20), residues: 741 sheet: -0.80 (0.14), residues: 1307 loop : -1.04 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 55 TYR 0.019 0.002 TYR B 91 PHE 0.027 0.002 PHE C 855 TRP 0.017 0.002 TRP C 886 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00557 (33256) covalent geometry : angle 0.67948 (45337) SS BOND : bond 0.00432 ( 47) SS BOND : angle 1.42837 ( 94) hydrogen bonds : bond 0.04809 ( 1165) hydrogen bonds : angle 5.49291 ( 3300) link_NAG-ASN : bond 0.00389 ( 22) link_NAG-ASN : angle 2.19921 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8424 Ramachandran restraints generated. 4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: A 900 MET cc_start: 0.8851 (mmm) cc_final: 0.8463 (mpp) REVERT: A 1101 HIS cc_start: 0.7227 (OUTLIER) cc_final: 0.6580 (m-70) REVERT: C 740 MET cc_start: 0.9252 (tpp) cc_final: 0.8761 (tpp) REVERT: D 74 MET cc_start: 0.8147 (mpp) cc_final: 0.7806 (mmm) REVERT: D 81 MET cc_start: 0.7112 (mtp) cc_final: 0.6769 (mmm) REVERT: E 215 CYS cc_start: 0.5160 (p) cc_final: 0.4898 (m) REVERT: F 2 MET cc_start: 0.4912 (ttt) cc_final: 0.4145 (tmm) REVERT: F 216 LYS cc_start: 0.8063 (mptt) cc_final: 0.7245 (tptt) REVERT: G 189 LYS cc_start: 0.7323 (pptt) cc_final: 0.6705 (pttt) REVERT: G 211 ASN cc_start: 0.9234 (m-40) cc_final: 0.8990 (t0) REVERT: H 220 LYS cc_start: 0.5178 (pptt) cc_final: 0.4711 (mmmt) REVERT: L 80 GLU cc_start: 0.7868 (pm20) cc_final: 0.7640 (pm20) REVERT: L 139 ASN cc_start: 0.6105 (p0) cc_final: 0.5839 (t0) outliers start: 45 outliers final: 38 residues processed: 143 average time/residue: 0.2403 time to fit residues: 52.3369 Evaluate side-chains 142 residues out of total 3723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain G residue 10 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 211 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 227 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN B 49 HIS ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN L 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.062469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037996 restraints weight = 294540.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.037734 restraints weight = 166040.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037782 restraints weight = 111240.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.038005 restraints weight = 88550.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.038325 restraints weight = 72981.125| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33325 Z= 0.220 Angle : 0.652 14.489 45497 Z= 0.335 Chirality : 0.044 0.209 5265 Planarity : 0.004 0.082 5857 Dihedral : 5.414 59.870 5027 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 1.20 % Allowed : 13.62 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4212 helix: 1.82 (0.20), residues: 743 sheet: -0.83 (0.14), residues: 1305 loop : -0.97 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 62 TYR 0.017 0.001 TYR H 80 PHE 0.018 0.001 PHE C 855 TRP 0.012 0.001 TRP F 50 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00486 (33256) covalent geometry : angle 0.64343 (45337) SS BOND : bond 0.00370 ( 47) SS BOND : angle 1.63476 ( 94) hydrogen bonds : bond 0.04504 ( 1165) hydrogen bonds : angle 5.38412 ( 3300) link_NAG-ASN : bond 0.00291 ( 22) link_NAG-ASN : angle 2.14665 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8016.15 seconds wall clock time: 138 minutes 2.90 seconds (8282.90 seconds total)