Starting phenix.real_space_refine on Fri Mar 6 10:42:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r8o_24320/03_2026/7r8o_24320.map" } resolution = 3.5 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= 0.021 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 141 5.16 5 C 19062 2.51 5 N 4941 2.21 5 O 5820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s 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: 29964 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "N" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 822 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 114, 818 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 829 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.07, per 1000 atoms: 0.24 Number of scatterers: 29964 At special positions: 0 Unit cell: (141.647, 139.909, 193.787, 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 141 16.00 O 5820 8.00 N 4941 7.00 C 19062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.01 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.05 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.01 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.05 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.04 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 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 "HETATM29962 O5 NAG E1310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 4 " " NAG Q 1 " - " FUC Q 5 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1134 " " NAG A1308 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 343 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 282 " " NAG E1305 " - " ASN E 616 " " NAG E1306 " - " ASN E 657 " " NAG E1307 " - " ASN E 717 " " NAG E1308 " - " ASN E 801 " " NAG E1309 " - " ASN E1098 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 343 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG Q 1 " - " ASN E 343 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 63 sheets defined 22.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.806A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 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 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.141A 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 removed outlier: 4.027A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) 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: 4.424A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.806A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.335A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 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 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.142A 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 removed outlier: 4.027A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) 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: 4.427A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.805A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.336A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 616 through 620 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.141A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 4.027A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.825A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU N 83 " --> pdb=" O GLU N 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.842A pdb=" N GLU P 83 " --> pdb=" O GLU P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.118A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.280A pdb=" N PHE A 43 " --> pdb=" O ARG E 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.592A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.915A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.211A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.486A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.127A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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: 5.918A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.406A 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 704 removed outlier: 3.753A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 719 through 728 removed outlier: 3.565A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.185A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.117A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.591A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.915A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.211A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.128A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) 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: 5.919A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.622A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.565A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'E' and resid 27 through 30 removed outlier: 4.117A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 203 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.592A pdb=" N VAL E 47 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.511A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP E 104 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 127 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE E 128 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE E 168 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL E 130 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N CYS E 166 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.914A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR E 612 " --> pdb=" O CYS E 649 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.127A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AE9, first strand: chain 'E' and resid 718 through 728 removed outlier: 3.566A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'E' and resid 1081 through 1082 removed outlier: 4.789A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF5, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AF6, first strand: chain 'H' and resid 56 through 59 removed outlier: 4.136A pdb=" N THR H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE H 52 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN H 39 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.599A pdb=" N ALA L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY L 89 " --> pdb=" O ASP L 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL L 33 " --> pdb=" O ARG L 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AG2, first strand: chain 'M' and resid 56 through 59 removed outlier: 4.135A pdb=" N THR M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE M 52 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET M 48 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN M 39 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.589A pdb=" N ALA N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY N 89 " --> pdb=" O ASP N 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL N 33 " --> pdb=" O ARG N 49 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG5, first strand: chain 'O' and resid 3 through 5 Processing sheet with id=AG6, first strand: chain 'O' and resid 18 through 20 Processing sheet with id=AG7, first strand: chain 'O' and resid 56 through 59 removed outlier: 4.135A pdb=" N THR O 56 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE O 52 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET O 48 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE O 34 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN O 39 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL O 89 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 9 through 11 removed outlier: 3.602A pdb=" N ALA P 11 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY P 89 " --> pdb=" O ASP P 34 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL P 33 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP P 35 " --> pdb=" O VAL P 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 19 through 24 removed outlier: 3.554A pdb=" N ILE P 75 " --> pdb=" O VAL P 19 " (cutoff:3.500A) 1136 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 2.60 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: 8368 1.33 - 1.46: 8471 1.46 - 1.59: 13614 1.59 - 1.72: 9 1.72 - 1.85: 183 Bond restraints: 30645 Sorted by residual: bond pdb=" C VAL P 19 " pdb=" CA AVAL P 19 " ideal model delta sigma weight residual 1.524 1.267 0.257 1.14e-02 7.69e+03 5.07e+02 bond pdb=" C VAL P 19 " pdb=" CA BVAL P 19 " ideal model delta sigma weight residual 1.524 1.267 0.257 1.14e-02 7.69e+03 5.07e+02 bond pdb=" N PRO A 812 " pdb=" CD PRO A 812 " ideal model delta sigma weight residual 1.473 1.290 0.183 1.40e-02 5.10e+03 1.70e+02 bond pdb=" C VAL N 19 " pdb=" CA AVAL N 19 " ideal model delta sigma weight residual 1.524 1.384 0.141 1.19e-02 7.06e+03 1.39e+02 bond pdb=" C VAL N 19 " pdb=" CA BVAL N 19 " ideal model delta sigma weight residual 1.524 1.384 0.141 1.19e-02 7.06e+03 1.39e+02 ... (remaining 30640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 40996 4.60 - 9.21: 608 9.21 - 13.81: 88 13.81 - 18.42: 5 18.42 - 23.02: 9 Bond angle restraints: 41706 Sorted by residual: angle pdb=" O VAL N 19 " pdb=" C VAL N 19 " pdb=" CA AVAL N 19 " ideal model delta sigma weight residual 120.51 134.33 -13.82 1.05e+00 9.07e-01 1.73e+02 angle pdb=" O VAL N 19 " pdb=" C VAL N 19 " pdb=" CA BVAL N 19 " ideal model delta sigma weight residual 120.51 134.33 -13.82 1.05e+00 9.07e-01 1.73e+02 angle pdb=" CA AVAL N 19 " pdb=" C VAL N 19 " pdb=" N THR N 20 " ideal model delta sigma weight residual 116.70 102.86 13.84 1.10e+00 8.26e-01 1.58e+02 angle pdb=" CA BVAL N 19 " pdb=" C VAL N 19 " pdb=" N THR N 20 " ideal model delta sigma weight residual 116.70 102.86 13.84 1.10e+00 8.26e-01 1.58e+02 angle pdb=" CA ARG B 214 " pdb=" CB ARG B 214 " pdb=" CG ARG B 214 " ideal model delta sigma weight residual 114.10 134.71 -20.61 2.00e+00 2.50e-01 1.06e+02 ... (remaining 41701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 17735 21.30 - 42.60: 841 42.60 - 63.89: 160 63.89 - 85.19: 51 85.19 - 106.49: 14 Dihedral angle restraints: 18801 sinusoidal: 7809 harmonic: 10992 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.52 -80.48 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS E 291 " pdb=" SG CYS E 291 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.53 -80.47 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -5.55 -80.45 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 18798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 4766 0.282 - 0.564: 56 0.564 - 0.846: 5 0.846 - 1.128: 0 1.128 - 1.410: 1 Chirality restraints: 4828 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.14e+02 chirality pdb=" C1 FUC Q 5 " pdb=" O6 NAG Q 1 " pdb=" C2 FUC Q 5 " pdb=" O5 FUC Q 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.00e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.40e+02 ... (remaining 4825 not shown) Planarity restraints: 5378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E1098 " 0.367 2.00e-02 2.50e+03 3.43e-01 1.47e+03 pdb=" CG ASN E1098 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN E1098 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN E1098 " -0.578 2.00e-02 2.50e+03 pdb=" C1 NAG E1309 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.295 2.00e-02 2.50e+03 2.53e-01 7.99e+02 pdb=" C7 NAG A1304 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.277 2.00e-02 2.50e+03 2.38e-01 7.06e+02 pdb=" C7 NAG F 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.039 2.00e-02 2.50e+03 ... (remaining 5375 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 122 2.48 - 3.09: 20065 3.09 - 3.69: 44284 3.69 - 4.30: 64667 4.30 - 4.90: 107191 Nonbonded interactions: 236329 Sorted by model distance: nonbonded pdb=" O GLN E 804 " pdb=" CD PRO E 817 " model vdw 1.876 3.440 nonbonded pdb=" O GLN B 804 " pdb=" CD PRO B 817 " model vdw 1.888 3.440 nonbonded pdb=" O ASP A1127 " pdb=" OD1 ASP A1127 " model vdw 1.908 3.040 nonbonded pdb=" ND2 ASN E1134 " pdb=" O5 NAG E1310 " model vdw 1.909 3.120 nonbonded pdb=" O GLN A 804 " pdb=" CD PRO A 817 " model vdw 1.983 3.440 ... (remaining 236324 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' selection = chain 'B' selection = (chain 'E' and resid 15 through 1308) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'L' and (resid 2 through 18 or resid 20 through 106)) selection = (chain 'N' and (resid 2 through 18 or resid 20 through 106)) selection = (chain 'P' and (resid 2 through 18 or resid 20 through 106)) } 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=0.50 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: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 28.560 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.010 0.875 30737 Z= 0.554 Angle : 1.528 49.612 41936 Z= 0.902 Chirality : 0.089 1.410 4828 Planarity : 0.016 0.253 5346 Dihedral : 13.226 106.490 11631 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.61 % Favored : 96.26 % Rotamer: Outliers : 1.03 % Allowed : 2.41 % Favored : 96.56 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.12), residues: 3747 helix: -0.04 (0.17), residues: 684 sheet: 1.01 (0.16), residues: 873 loop : -0.69 (0.12), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A 214 TYR 0.095 0.005 TYR H 100D PHE 0.068 0.005 PHE E 275 TRP 0.059 0.004 TRP M 47 HIS 0.013 0.003 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00846 (30645) covalent geometry : angle 1.48327 (41706) SS BOND : bond 0.00961 ( 46) SS BOND : angle 3.44362 ( 92) hydrogen bonds : bond 0.19677 ( 1136) hydrogen bonds : angle 9.00108 ( 3081) link_ALPHA1-6 : bond 0.00128 ( 1) link_ALPHA1-6 : angle 0.26826 ( 3) link_BETA1-4 : bond 0.00580 ( 10) link_BETA1-4 : angle 3.84595 ( 30) link_BETA1-6 : bond 0.01512 ( 3) link_BETA1-6 : angle 3.28220 ( 9) link_NAG-ASN : bond 0.15525 ( 32) link_NAG-ASN : angle 6.85959 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 616 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8310 (m-90) cc_final: 0.7804 (m-90) REVERT: A 118 LEU cc_start: 0.7528 (tp) cc_final: 0.7319 (tp) REVERT: A 129 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7201 (mttm) REVERT: A 405 ASP cc_start: 0.8149 (m-30) cc_final: 0.7657 (t0) REVERT: A 779 GLN cc_start: 0.8206 (tt0) cc_final: 0.7999 (mt0) REVERT: B 28 TYR cc_start: 0.7820 (m-80) cc_final: 0.7061 (m-10) REVERT: B 405 ASP cc_start: 0.8187 (m-30) cc_final: 0.7710 (t0) REVERT: B 493 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6898 (mm110) REVERT: B 578 ASP cc_start: 0.8173 (t70) cc_final: 0.7859 (t0) REVERT: B 620 VAL cc_start: 0.9120 (t) cc_final: 0.8624 (t) REVERT: B 751 ASN cc_start: 0.8715 (m-40) cc_final: 0.8503 (m-40) REVERT: B 1126 CYS cc_start: 0.6278 (p) cc_final: 0.6007 (p) REVERT: E 129 LYS cc_start: 0.7342 (mtpt) cc_final: 0.7122 (mttm) REVERT: E 354 ASN cc_start: 0.8376 (t0) cc_final: 0.8168 (m-40) REVERT: E 405 ASP cc_start: 0.8294 (m-30) cc_final: 0.7894 (t0) REVERT: E 755 GLN cc_start: 0.8415 (tt0) cc_final: 0.8164 (tt0) REVERT: L 20 THR cc_start: 0.8666 (m) cc_final: 0.8439 (t) REVERT: L 34 ASP cc_start: 0.8395 (m-30) cc_final: 0.7862 (m-30) REVERT: M 13 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8396 (mmtt) REVERT: M 48 MET cc_start: 0.8399 (ptp) cc_final: 0.7988 (ptp) REVERT: N 34 ASP cc_start: 0.8222 (m-30) cc_final: 0.7709 (m-30) REVERT: O 13 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8294 (mmtt) REVERT: O 48 MET cc_start: 0.8201 (ptp) cc_final: 0.7747 (ptp) REVERT: P 34 ASP cc_start: 0.8314 (m-30) cc_final: 0.7820 (m-30) REVERT: P 103 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7841 (mmmt) outliers start: 27 outliers final: 7 residues processed: 632 average time/residue: 0.1703 time to fit residues: 176.5463 Evaluate side-chains 409 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 402 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 955 ASN A 957 GLN A1005 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B 774 GLN B 777 ASN B 804 GLN B 957 GLN B 969 ASN B1005 GLN B1135 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN E 777 ASN E 804 GLN E 957 GLN E1005 GLN L 6 GLN N 6 GLN P 6 GLN P 79 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103640 restraints weight = 53947.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107869 restraints weight = 24405.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110677 restraints weight = 14509.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.112531 restraints weight = 10186.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113722 restraints weight = 8013.569| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30737 Z= 0.151 Angle : 0.706 12.013 41936 Z= 0.362 Chirality : 0.047 0.347 4828 Planarity : 0.006 0.070 5346 Dihedral : 7.145 67.618 5093 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.62 % Allowed : 8.75 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.13), residues: 3747 helix: 1.76 (0.20), residues: 663 sheet: 0.98 (0.17), residues: 867 loop : -0.73 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 214 TYR 0.031 0.002 TYR O 100E PHE 0.026 0.002 PHE B 220 TRP 0.010 0.001 TRP B 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00331 (30645) covalent geometry : angle 0.67566 (41706) SS BOND : bond 0.00399 ( 46) SS BOND : angle 2.28438 ( 92) hydrogen bonds : bond 0.04729 ( 1136) hydrogen bonds : angle 6.69970 ( 3081) link_ALPHA1-6 : bond 0.00571 ( 1) link_ALPHA1-6 : angle 1.30130 ( 3) link_BETA1-4 : bond 0.01121 ( 10) link_BETA1-4 : angle 3.33782 ( 30) link_BETA1-6 : bond 0.00296 ( 3) link_BETA1-6 : angle 1.72680 ( 9) link_NAG-ASN : bond 0.00616 ( 32) link_NAG-ASN : angle 3.25512 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 423 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8291 (m-90) cc_final: 0.7811 (m-90) REVERT: A 129 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6907 (mtpt) REVERT: A 405 ASP cc_start: 0.8144 (m-30) cc_final: 0.7782 (t0) REVERT: A 774 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7736 (mm-40) REVERT: B 97 LYS cc_start: 0.4920 (tptt) cc_final: 0.4705 (tptp) REVERT: B 269 TYR cc_start: 0.6973 (m-80) cc_final: 0.6753 (m-80) REVERT: B 378 LYS cc_start: 0.8321 (tttp) cc_final: 0.7789 (ttpt) REVERT: B 405 ASP cc_start: 0.8154 (m-30) cc_final: 0.7810 (t0) REVERT: B 578 ASP cc_start: 0.8075 (t70) cc_final: 0.7677 (t0) REVERT: B 751 ASN cc_start: 0.8666 (m-40) cc_final: 0.8464 (m-40) REVERT: E 129 LYS cc_start: 0.7034 (mtpt) cc_final: 0.6770 (mttm) REVERT: E 405 ASP cc_start: 0.8290 (m-30) cc_final: 0.7944 (t0) REVERT: E 462 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8422 (mmtp) REVERT: E 731 MET cc_start: 0.9049 (ptm) cc_final: 0.8488 (ptm) REVERT: E 1135 ASN cc_start: 0.8454 (t0) cc_final: 0.8186 (t0) REVERT: H 18 VAL cc_start: 0.7014 (p) cc_final: 0.6769 (m) REVERT: L 79 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6493 (mm110) REVERT: O 13 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8325 (mmtt) REVERT: P 103 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7911 (mttp) outliers start: 46 outliers final: 27 residues processed: 457 average time/residue: 0.1739 time to fit residues: 131.5469 Evaluate side-chains 375 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 361 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 286 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 901 GLN A 969 ASN A1005 GLN B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 969 ASN E 121 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN E1005 GLN H 39 GLN L 37 GLN N 37 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099029 restraints weight = 53960.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102389 restraints weight = 28483.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104648 restraints weight = 18521.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106111 restraints weight = 13808.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107097 restraints weight = 11350.400| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 30737 Z= 0.244 Angle : 0.722 12.004 41936 Z= 0.368 Chirality : 0.049 0.349 4828 Planarity : 0.005 0.052 5346 Dihedral : 6.379 58.773 5088 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.12 % Allowed : 11.87 % Favored : 86.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.13), residues: 3747 helix: 1.77 (0.20), residues: 690 sheet: 0.82 (0.17), residues: 837 loop : -0.85 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 94 TYR 0.038 0.002 TYR B 904 PHE 0.025 0.002 PHE E 490 TRP 0.019 0.002 TRP H 47 HIS 0.016 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00571 (30645) covalent geometry : angle 0.69448 (41706) SS BOND : bond 0.00396 ( 46) SS BOND : angle 2.02492 ( 92) hydrogen bonds : bond 0.04740 ( 1136) hydrogen bonds : angle 6.14761 ( 3081) link_ALPHA1-6 : bond 0.00704 ( 1) link_ALPHA1-6 : angle 1.30578 ( 3) link_BETA1-4 : bond 0.00990 ( 10) link_BETA1-4 : angle 3.37297 ( 30) link_BETA1-6 : bond 0.00174 ( 3) link_BETA1-6 : angle 1.91064 ( 9) link_NAG-ASN : bond 0.00577 ( 32) link_NAG-ASN : angle 3.16103 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 393 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8265 (m-30) cc_final: 0.7917 (t0) REVERT: B 97 LYS cc_start: 0.4826 (tptt) cc_final: 0.4597 (tptp) REVERT: B 316 SER cc_start: 0.8967 (t) cc_final: 0.8451 (p) REVERT: B 405 ASP cc_start: 0.8270 (m-30) cc_final: 0.7860 (t0) REVERT: B 467 ASP cc_start: 0.6861 (p0) cc_final: 0.6576 (p0) REVERT: B 468 ILE cc_start: 0.8577 (pt) cc_final: 0.8223 (tt) REVERT: B 578 ASP cc_start: 0.8175 (t70) cc_final: 0.7911 (t0) REVERT: B 869 MET cc_start: 0.8495 (mtm) cc_final: 0.8054 (mtm) REVERT: E 52 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8374 (tm-30) REVERT: E 405 ASP cc_start: 0.8442 (m-30) cc_final: 0.8109 (t0) REVERT: E 462 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8504 (mmtp) REVERT: E 731 MET cc_start: 0.9043 (ptm) cc_final: 0.8740 (ptm) REVERT: E 869 MET cc_start: 0.8307 (mtp) cc_final: 0.8036 (mtm) REVERT: E 1135 ASN cc_start: 0.8449 (t0) cc_final: 0.8110 (t0) REVERT: H 90 TYR cc_start: 0.7709 (m-80) cc_final: 0.7279 (m-80) REVERT: H 100 TYR cc_start: 0.8263 (m-80) cc_final: 0.7866 (m-80) REVERT: L 34 ASP cc_start: 0.8471 (m-30) cc_final: 0.7881 (m-30) REVERT: L 86 TYR cc_start: 0.7421 (m-10) cc_final: 0.7106 (m-80) REVERT: M 100 TYR cc_start: 0.6918 (t80) cc_final: 0.6676 (t80) REVERT: N 34 ASP cc_start: 0.8450 (m-30) cc_final: 0.7861 (m-30) REVERT: N 39 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: N 79 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6643 (mm110) REVERT: O 48 MET cc_start: 0.8788 (ptm) cc_final: 0.8584 (ptp) REVERT: O 100 TYR cc_start: 0.8374 (m-80) cc_final: 0.8100 (m-10) REVERT: P 34 ASP cc_start: 0.8470 (m-30) cc_final: 0.7997 (m-30) REVERT: P 65 LEU cc_start: 0.8545 (tp) cc_final: 0.8345 (tt) REVERT: P 79 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6590 (mm110) REVERT: P 103 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7922 (mmmt) outliers start: 62 outliers final: 43 residues processed: 441 average time/residue: 0.1774 time to fit residues: 127.5367 Evaluate side-chains 370 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 1097 SER Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 310 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 292 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 359 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 804 GLN A1005 GLN A1135 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN E 394 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN H 39 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102772 restraints weight = 52665.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106508 restraints weight = 26277.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109006 restraints weight = 16506.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110614 restraints weight = 12021.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111676 restraints weight = 9697.487| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30737 Z= 0.131 Angle : 0.610 11.648 41936 Z= 0.308 Chirality : 0.045 0.308 4828 Planarity : 0.004 0.047 5346 Dihedral : 5.999 55.133 5085 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.97 % Allowed : 13.00 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.13), residues: 3747 helix: 1.99 (0.20), residues: 690 sheet: 0.64 (0.16), residues: 915 loop : -0.75 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.032 0.002 TYR H 100D PHE 0.017 0.001 PHE E 157 TRP 0.014 0.001 TRP O 47 HIS 0.009 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00300 (30645) covalent geometry : angle 0.58183 (41706) SS BOND : bond 0.00285 ( 46) SS BOND : angle 1.91518 ( 92) hydrogen bonds : bond 0.04009 ( 1136) hydrogen bonds : angle 5.85437 ( 3081) link_ALPHA1-6 : bond 0.00970 ( 1) link_ALPHA1-6 : angle 1.14791 ( 3) link_BETA1-4 : bond 0.00999 ( 10) link_BETA1-4 : angle 3.12365 ( 30) link_BETA1-6 : bond 0.00264 ( 3) link_BETA1-6 : angle 1.62762 ( 9) link_NAG-ASN : bond 0.00376 ( 32) link_NAG-ASN : angle 2.94836 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 371 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8230 (m-30) cc_final: 0.7954 (m-30) REVERT: B 97 LYS cc_start: 0.4886 (tptt) cc_final: 0.4673 (tptp) REVERT: B 316 SER cc_start: 0.8944 (t) cc_final: 0.8442 (p) REVERT: B 389 ASP cc_start: 0.7890 (t0) cc_final: 0.7688 (t0) REVERT: B 405 ASP cc_start: 0.8260 (m-30) cc_final: 0.7990 (m-30) REVERT: B 467 ASP cc_start: 0.6906 (p0) cc_final: 0.6562 (p0) REVERT: B 468 ILE cc_start: 0.8669 (pt) cc_final: 0.8262 (tt) REVERT: B 578 ASP cc_start: 0.8116 (t70) cc_final: 0.7873 (t0) REVERT: B 664 ILE cc_start: 0.8336 (mm) cc_final: 0.7985 (mm) REVERT: B 1083 HIS cc_start: 0.7827 (t70) cc_final: 0.7524 (t70) REVERT: E 269 TYR cc_start: 0.7249 (m-80) cc_final: 0.6986 (m-80) REVERT: E 405 ASP cc_start: 0.8437 (m-30) cc_final: 0.7994 (m-30) REVERT: E 462 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8368 (mmmt) REVERT: E 664 ILE cc_start: 0.8216 (mm) cc_final: 0.7896 (mm) REVERT: E 731 MET cc_start: 0.9046 (ptm) cc_final: 0.8694 (ptm) REVERT: E 1135 ASN cc_start: 0.8330 (t0) cc_final: 0.8008 (t0) REVERT: H 47 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.8349 (t60) REVERT: H 94 ARG cc_start: 0.7817 (ptt90) cc_final: 0.7529 (ptt90) REVERT: H 100 TYR cc_start: 0.8192 (m-80) cc_final: 0.7575 (m-80) REVERT: L 34 ASP cc_start: 0.8390 (m-30) cc_final: 0.7797 (m-30) REVERT: L 86 TYR cc_start: 0.7405 (m-10) cc_final: 0.7119 (m-80) REVERT: M 94 ARG cc_start: 0.8226 (ptt90) cc_final: 0.7869 (ptt90) REVERT: M 100 TYR cc_start: 0.6567 (t80) cc_final: 0.6328 (t80) REVERT: N 34 ASP cc_start: 0.8255 (m-30) cc_final: 0.7612 (m-30) REVERT: N 39 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.8166 (mmm-85) REVERT: O 100 TYR cc_start: 0.8273 (m-80) cc_final: 0.7957 (m-10) REVERT: P 34 ASP cc_start: 0.8436 (m-30) cc_final: 0.8006 (m-30) REVERT: P 38 GLN cc_start: 0.7455 (tt0) cc_final: 0.6645 (tp40) REVERT: P 79 GLN cc_start: 0.6802 (mm-40) cc_final: 0.6571 (mm110) REVERT: P 103 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7952 (mmmt) outliers start: 57 outliers final: 34 residues processed: 412 average time/residue: 0.1801 time to fit residues: 121.2606 Evaluate side-chains 377 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 131 optimal weight: 1.9990 chunk 337 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN N 38 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.120618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094053 restraints weight = 54106.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097272 restraints weight = 28586.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099426 restraints weight = 18619.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100812 restraints weight = 13913.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101750 restraints weight = 11481.177| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 30737 Z= 0.298 Angle : 0.747 12.879 41936 Z= 0.376 Chirality : 0.049 0.318 4828 Planarity : 0.005 0.051 5346 Dihedral : 6.295 59.942 5085 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.25 % Allowed : 12.75 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.13), residues: 3747 helix: 1.70 (0.20), residues: 693 sheet: 0.63 (0.17), residues: 867 loop : -1.00 (0.13), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1107 TYR 0.045 0.003 TYR A 904 PHE 0.021 0.002 PHE B 133 TRP 0.031 0.002 TRP M 47 HIS 0.009 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00709 (30645) covalent geometry : angle 0.71758 (41706) SS BOND : bond 0.00342 ( 46) SS BOND : angle 2.39390 ( 92) hydrogen bonds : bond 0.04650 ( 1136) hydrogen bonds : angle 6.02988 ( 3081) link_ALPHA1-6 : bond 0.00651 ( 1) link_ALPHA1-6 : angle 1.30926 ( 3) link_BETA1-4 : bond 0.00940 ( 10) link_BETA1-4 : angle 3.25000 ( 30) link_BETA1-6 : bond 0.00250 ( 3) link_BETA1-6 : angle 1.97502 ( 9) link_NAG-ASN : bond 0.00530 ( 32) link_NAG-ASN : angle 3.27565 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 367 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 316 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8815 (p) REVERT: A 405 ASP cc_start: 0.8343 (m-30) cc_final: 0.8001 (t0) REVERT: A 516 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 697 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7705 (ttt) REVERT: B 316 SER cc_start: 0.9027 (t) cc_final: 0.8487 (p) REVERT: B 405 ASP cc_start: 0.8328 (m-30) cc_final: 0.7922 (t0) REVERT: B 467 ASP cc_start: 0.7169 (p0) cc_final: 0.6863 (p0) REVERT: B 468 ILE cc_start: 0.8748 (pt) cc_final: 0.8423 (mt) REVERT: B 484 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: B 664 ILE cc_start: 0.8570 (mm) cc_final: 0.8156 (mm) REVERT: B 869 MET cc_start: 0.8470 (mtm) cc_final: 0.8035 (mtm) REVERT: B 1083 HIS cc_start: 0.8159 (t70) cc_final: 0.7819 (t70) REVERT: E 52 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 242 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6975 (pp) REVERT: E 307 THR cc_start: 0.8760 (m) cc_final: 0.8483 (p) REVERT: E 316 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8645 (p) REVERT: E 370 ASN cc_start: 0.8206 (t0) cc_final: 0.7957 (t0) REVERT: E 405 ASP cc_start: 0.8457 (m-30) cc_final: 0.8124 (t0) REVERT: E 664 ILE cc_start: 0.8469 (mm) cc_final: 0.8055 (mm) REVERT: E 1135 ASN cc_start: 0.8453 (t0) cc_final: 0.8060 (t0) REVERT: H 47 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.8086 (t60) REVERT: H 91 TYR cc_start: 0.7814 (m-80) cc_final: 0.7381 (m-80) REVERT: H 96 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8066 (mm-30) REVERT: L 34 ASP cc_start: 0.8650 (m-30) cc_final: 0.8152 (m-30) REVERT: L 86 TYR cc_start: 0.7510 (m-10) cc_final: 0.7255 (m-80) REVERT: M 96 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7868 (mm-30) REVERT: M 100 TYR cc_start: 0.8397 (m-80) cc_final: 0.7999 (m-80) REVERT: N 34 ASP cc_start: 0.8543 (m-30) cc_final: 0.8237 (m-30) REVERT: N 39 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8293 (mmm-85) REVERT: O 47 TRP cc_start: 0.8511 (t-100) cc_final: 0.8137 (t60) REVERT: O 94 ARG cc_start: 0.7822 (ptt90) cc_final: 0.6942 (ptt90) REVERT: O 96 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7355 (mm-30) REVERT: O 100 TYR cc_start: 0.8365 (m-80) cc_final: 0.8135 (m-10) REVERT: P 34 ASP cc_start: 0.8642 (m-30) cc_final: 0.8164 (m-30) REVERT: P 79 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6793 (mm110) REVERT: P 103 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8110 (mttp) outliers start: 98 outliers final: 60 residues processed: 444 average time/residue: 0.1890 time to fit residues: 134.6421 Evaluate side-chains 392 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 326 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 781 VAL Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 92 CYS Chi-restraints excluded: chain M residue 102 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 18 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 33 optimal weight: 0.0060 chunk 166 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 231 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.127565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100534 restraints weight = 52792.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104216 restraints weight = 26213.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106658 restraints weight = 16430.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108250 restraints weight = 11974.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.109249 restraints weight = 9666.588| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30737 Z= 0.121 Angle : 0.610 11.754 41936 Z= 0.308 Chirality : 0.045 0.285 4828 Planarity : 0.004 0.045 5346 Dihedral : 5.863 54.673 5085 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.28 % Allowed : 14.53 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.14), residues: 3747 helix: 1.97 (0.20), residues: 690 sheet: 0.50 (0.17), residues: 909 loop : -0.87 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.039 0.002 TYR H 100D PHE 0.015 0.001 PHE E 559 TRP 0.021 0.001 TRP M 47 HIS 0.006 0.001 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (30645) covalent geometry : angle 0.58484 (41706) SS BOND : bond 0.00277 ( 46) SS BOND : angle 1.64894 ( 92) hydrogen bonds : bond 0.03830 ( 1136) hydrogen bonds : angle 5.67862 ( 3081) link_ALPHA1-6 : bond 0.00929 ( 1) link_ALPHA1-6 : angle 1.08567 ( 3) link_BETA1-4 : bond 0.01074 ( 10) link_BETA1-4 : angle 2.90740 ( 30) link_BETA1-6 : bond 0.00350 ( 3) link_BETA1-6 : angle 1.56615 ( 9) link_NAG-ASN : bond 0.00366 ( 32) link_NAG-ASN : angle 2.93166 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 351 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8420 (tm-30) REVERT: A 405 ASP cc_start: 0.8313 (m-30) cc_final: 0.8052 (m-30) REVERT: A 900 MET cc_start: 0.8639 (mtp) cc_final: 0.8425 (ttm) REVERT: B 405 ASP cc_start: 0.8265 (m-30) cc_final: 0.7798 (t0) REVERT: B 467 ASP cc_start: 0.7088 (p0) cc_final: 0.6796 (p0) REVERT: B 468 ILE cc_start: 0.8730 (pt) cc_final: 0.8449 (mt) REVERT: B 664 ILE cc_start: 0.8403 (mm) cc_final: 0.8055 (mm) REVERT: B 1083 HIS cc_start: 0.7977 (t70) cc_final: 0.7549 (t70) REVERT: E 52 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8411 (tm-30) REVERT: E 405 ASP cc_start: 0.8388 (m-30) cc_final: 0.7963 (m-30) REVERT: E 462 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8397 (mmmt) REVERT: E 474 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7889 (tp40) REVERT: E 484 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7490 (pt0) REVERT: E 664 ILE cc_start: 0.8339 (mm) cc_final: 0.8017 (mm) REVERT: E 697 MET cc_start: 0.8204 (ptm) cc_final: 0.7902 (ttp) REVERT: E 900 MET cc_start: 0.8666 (ttm) cc_final: 0.8409 (ttm) REVERT: E 1135 ASN cc_start: 0.8453 (t0) cc_final: 0.8066 (t0) REVERT: H 47 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.8198 (t60) REVERT: H 100 TYR cc_start: 0.8324 (m-80) cc_final: 0.8099 (m-80) REVERT: L 34 ASP cc_start: 0.8502 (m-30) cc_final: 0.7836 (m-30) REVERT: L 86 TYR cc_start: 0.7342 (m-10) cc_final: 0.7106 (m-80) REVERT: M 100 ARG cc_start: 0.8464 (tmm-80) cc_final: 0.8254 (tmm-80) REVERT: M 100 TYR cc_start: 0.8373 (m-80) cc_final: 0.8072 (m-80) REVERT: N 34 ASP cc_start: 0.8220 (m-30) cc_final: 0.7592 (m-30) REVERT: N 39 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8236 (mmm-85) REVERT: O 47 TRP cc_start: 0.8445 (t-100) cc_final: 0.8075 (t60) REVERT: O 100 TYR cc_start: 0.8225 (m-80) cc_final: 0.7939 (m-80) REVERT: P 34 ASP cc_start: 0.8544 (m-30) cc_final: 0.8085 (m-30) REVERT: P 79 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6660 (mm110) REVERT: P 103 LYS cc_start: 0.8286 (mtpt) cc_final: 0.8061 (mttp) outliers start: 67 outliers final: 36 residues processed: 401 average time/residue: 0.1825 time to fit residues: 117.4630 Evaluate side-chains 365 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 326 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 206 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 366 optimal weight: 0.1980 chunk 285 optimal weight: 0.7980 chunk 159 optimal weight: 0.0030 chunk 91 optimal weight: 4.9990 chunk 300 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN E1005 GLN E1106 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100835 restraints weight = 53170.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104237 restraints weight = 27460.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106481 restraints weight = 17573.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107957 restraints weight = 12972.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108925 restraints weight = 10555.030| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30737 Z= 0.116 Angle : 0.595 11.836 41936 Z= 0.299 Chirality : 0.044 0.295 4828 Planarity : 0.004 0.043 5346 Dihedral : 5.711 55.146 5085 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.87 % Allowed : 15.31 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.14), residues: 3747 helix: 2.02 (0.20), residues: 693 sheet: 0.55 (0.17), residues: 903 loop : -0.80 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.046 0.002 TYR O 100D PHE 0.019 0.001 PHE N 95C TRP 0.045 0.001 TRP M 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00265 (30645) covalent geometry : angle 0.56717 (41706) SS BOND : bond 0.00236 ( 46) SS BOND : angle 1.96394 ( 92) hydrogen bonds : bond 0.03683 ( 1136) hydrogen bonds : angle 5.57055 ( 3081) link_ALPHA1-6 : bond 0.00773 ( 1) link_ALPHA1-6 : angle 1.19247 ( 3) link_BETA1-4 : bond 0.00962 ( 10) link_BETA1-4 : angle 2.87856 ( 30) link_BETA1-6 : bond 0.00319 ( 3) link_BETA1-6 : angle 1.53270 ( 9) link_NAG-ASN : bond 0.00328 ( 32) link_NAG-ASN : angle 2.86465 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 405 ASP cc_start: 0.8303 (m-30) cc_final: 0.8056 (m-30) REVERT: A 471 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 405 ASP cc_start: 0.8251 (m-30) cc_final: 0.8046 (m-30) REVERT: B 467 ASP cc_start: 0.7136 (p0) cc_final: 0.6817 (p0) REVERT: B 468 ILE cc_start: 0.8735 (pt) cc_final: 0.8474 (mt) REVERT: B 664 ILE cc_start: 0.8420 (mm) cc_final: 0.8058 (mm) REVERT: B 1083 HIS cc_start: 0.7950 (t70) cc_final: 0.7538 (t70) REVERT: E 52 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8395 (tm-30) REVERT: E 405 ASP cc_start: 0.8363 (m-30) cc_final: 0.7942 (m-30) REVERT: E 462 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8434 (mmmt) REVERT: E 484 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: E 664 ILE cc_start: 0.8369 (mm) cc_final: 0.8029 (mm) REVERT: E 697 MET cc_start: 0.8198 (ptm) cc_final: 0.7889 (ttp) REVERT: E 900 MET cc_start: 0.8654 (ttm) cc_final: 0.8439 (ttm) REVERT: E 1135 ASN cc_start: 0.8455 (t0) cc_final: 0.8075 (t0) REVERT: H 48 MET cc_start: 0.8639 (ptp) cc_final: 0.8364 (ptm) REVERT: H 59 TYR cc_start: 0.8523 (m-80) cc_final: 0.8160 (m-80) REVERT: H 100 TYR cc_start: 0.8262 (m-80) cc_final: 0.7963 (m-80) REVERT: L 34 ASP cc_start: 0.8453 (m-30) cc_final: 0.7848 (m-30) REVERT: L 86 TYR cc_start: 0.7411 (m-10) cc_final: 0.7167 (m-80) REVERT: M 48 MET cc_start: 0.8629 (ptp) cc_final: 0.8344 (ptm) REVERT: M 100 ARG cc_start: 0.8466 (tmm-80) cc_final: 0.8250 (tmm-80) REVERT: N 34 ASP cc_start: 0.8273 (m-30) cc_final: 0.7706 (m-30) REVERT: N 39 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8269 (mmm-85) REVERT: O 6 GLN cc_start: 0.7944 (pm20) cc_final: 0.7503 (pm20) REVERT: O 10 GLU cc_start: 0.7071 (mp0) cc_final: 0.6867 (mp0) REVERT: O 100 ARG cc_start: 0.8418 (tmm-80) cc_final: 0.8182 (tmm-80) REVERT: O 100 TYR cc_start: 0.8194 (m-80) cc_final: 0.7943 (m-80) REVERT: P 34 ASP cc_start: 0.8533 (m-30) cc_final: 0.8113 (m-30) REVERT: P 79 GLN cc_start: 0.6893 (mm-40) cc_final: 0.6676 (mm110) REVERT: P 103 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8130 (mttp) outliers start: 54 outliers final: 43 residues processed: 374 average time/residue: 0.1834 time to fit residues: 110.3749 Evaluate side-chains 360 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 316 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 172 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 276 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099683 restraints weight = 53630.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103043 restraints weight = 27734.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105275 restraints weight = 17758.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106714 restraints weight = 13114.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107570 restraints weight = 10734.024| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30737 Z= 0.142 Angle : 0.598 12.071 41936 Z= 0.301 Chirality : 0.045 0.305 4828 Planarity : 0.004 0.044 5346 Dihedral : 5.668 55.777 5085 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.12 % Allowed : 15.71 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.14), residues: 3747 helix: 2.04 (0.21), residues: 693 sheet: 0.57 (0.17), residues: 903 loop : -0.79 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.048 0.002 TYR M 100D PHE 0.021 0.001 PHE N 95C TRP 0.034 0.001 TRP M 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00335 (30645) covalent geometry : angle 0.57081 (41706) SS BOND : bond 0.00228 ( 46) SS BOND : angle 1.98400 ( 92) hydrogen bonds : bond 0.03704 ( 1136) hydrogen bonds : angle 5.52706 ( 3081) link_ALPHA1-6 : bond 0.00608 ( 1) link_ALPHA1-6 : angle 1.22614 ( 3) link_BETA1-4 : bond 0.00991 ( 10) link_BETA1-4 : angle 2.89543 ( 30) link_BETA1-6 : bond 0.00174 ( 3) link_BETA1-6 : angle 1.48875 ( 9) link_NAG-ASN : bond 0.00319 ( 32) link_NAG-ASN : angle 2.85324 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 327 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8401 (tm-30) REVERT: A 316 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8802 (p) REVERT: A 405 ASP cc_start: 0.8314 (m-30) cc_final: 0.8063 (m-30) REVERT: A 471 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 405 ASP cc_start: 0.8299 (m-30) cc_final: 0.8093 (m-30) REVERT: B 467 ASP cc_start: 0.7231 (p0) cc_final: 0.6878 (p0) REVERT: B 664 ILE cc_start: 0.8438 (mm) cc_final: 0.8081 (mm) REVERT: B 1083 HIS cc_start: 0.7977 (t70) cc_final: 0.7616 (t70) REVERT: E 52 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8400 (tm-30) REVERT: E 405 ASP cc_start: 0.8379 (m-30) cc_final: 0.7979 (m-30) REVERT: E 462 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8434 (mmmt) REVERT: E 484 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: E 664 ILE cc_start: 0.8385 (mm) cc_final: 0.8046 (mm) REVERT: E 697 MET cc_start: 0.8248 (ptm) cc_final: 0.7928 (ttp) REVERT: E 900 MET cc_start: 0.8665 (ttm) cc_final: 0.8424 (ttm) REVERT: E 1135 ASN cc_start: 0.8459 (t0) cc_final: 0.8163 (t0) REVERT: H 47 TRP cc_start: 0.8397 (t60) cc_final: 0.8179 (t60) REVERT: H 48 MET cc_start: 0.8669 (ptp) cc_final: 0.8326 (ptm) REVERT: H 59 TYR cc_start: 0.8523 (m-80) cc_final: 0.8138 (m-80) REVERT: L 34 ASP cc_start: 0.8469 (m-30) cc_final: 0.7833 (m-30) REVERT: L 86 TYR cc_start: 0.7419 (m-10) cc_final: 0.7185 (m-80) REVERT: M 94 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7675 (ptt90) REVERT: N 34 ASP cc_start: 0.8320 (m-30) cc_final: 0.7710 (m-30) REVERT: N 39 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8287 (mmm-85) REVERT: O 6 GLN cc_start: 0.7970 (pm20) cc_final: 0.7473 (pm20) REVERT: O 10 GLU cc_start: 0.7058 (mp0) cc_final: 0.6832 (mp0) REVERT: O 47 TRP cc_start: 0.8460 (t-100) cc_final: 0.8102 (t60) REVERT: O 59 TYR cc_start: 0.8403 (m-80) cc_final: 0.8203 (m-80) REVERT: O 90 TYR cc_start: 0.7594 (m-80) cc_final: 0.7373 (m-80) REVERT: O 100 ARG cc_start: 0.8416 (tmm-80) cc_final: 0.8180 (tmm-80) REVERT: O 100 TYR cc_start: 0.8248 (m-80) cc_final: 0.8018 (m-80) REVERT: P 34 ASP cc_start: 0.8554 (m-30) cc_final: 0.8141 (m-30) REVERT: P 79 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6769 (mm110) outliers start: 62 outliers final: 45 residues processed: 378 average time/residue: 0.1895 time to fit residues: 115.3448 Evaluate side-chains 360 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 24 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 365 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 373 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 275 optimal weight: 0.6980 chunk 264 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A1106 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100862 restraints weight = 53238.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104236 restraints weight = 27503.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106479 restraints weight = 17617.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107930 restraints weight = 13001.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108895 restraints weight = 10613.076| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30737 Z= 0.122 Angle : 0.601 16.595 41936 Z= 0.304 Chirality : 0.044 0.303 4828 Planarity : 0.004 0.044 5346 Dihedral : 5.591 54.898 5085 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.91 % Allowed : 16.21 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3747 helix: 2.23 (0.21), residues: 672 sheet: 0.49 (0.17), residues: 912 loop : -0.68 (0.14), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.045 0.002 TYR O 100D PHE 0.020 0.001 PHE N 95C TRP 0.042 0.001 TRP M 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00282 (30645) covalent geometry : angle 0.56720 (41706) SS BOND : bond 0.00231 ( 46) SS BOND : angle 2.81951 ( 92) hydrogen bonds : bond 0.03624 ( 1136) hydrogen bonds : angle 5.47473 ( 3081) link_ALPHA1-6 : bond 0.00639 ( 1) link_ALPHA1-6 : angle 1.25116 ( 3) link_BETA1-4 : bond 0.00948 ( 10) link_BETA1-4 : angle 2.82599 ( 30) link_BETA1-6 : bond 0.00294 ( 3) link_BETA1-6 : angle 1.45961 ( 9) link_NAG-ASN : bond 0.00327 ( 32) link_NAG-ASN : angle 2.79460 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 316 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 405 ASP cc_start: 0.8300 (m-30) cc_final: 0.8064 (m-30) REVERT: A 471 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7755 (mm-30) REVERT: B 405 ASP cc_start: 0.8270 (m-30) cc_final: 0.8067 (m-30) REVERT: B 467 ASP cc_start: 0.7240 (p0) cc_final: 0.6872 (p0) REVERT: B 664 ILE cc_start: 0.8406 (mm) cc_final: 0.8061 (mm) REVERT: B 755 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: B 1083 HIS cc_start: 0.7951 (t70) cc_final: 0.7605 (t70) REVERT: E 52 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8395 (tm-30) REVERT: E 405 ASP cc_start: 0.8362 (m-30) cc_final: 0.7936 (m-30) REVERT: E 462 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8446 (mmmt) REVERT: E 484 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: E 664 ILE cc_start: 0.8355 (mm) cc_final: 0.8036 (mm) REVERT: E 697 MET cc_start: 0.8198 (ptm) cc_final: 0.7924 (ttp) REVERT: E 1135 ASN cc_start: 0.8455 (t0) cc_final: 0.8157 (t0) REVERT: H 48 MET cc_start: 0.8647 (ptp) cc_final: 0.7770 (ptm) REVERT: H 59 TYR cc_start: 0.8510 (m-80) cc_final: 0.8120 (m-80) REVERT: L 34 ASP cc_start: 0.8431 (m-30) cc_final: 0.7811 (m-30) REVERT: L 86 TYR cc_start: 0.7407 (m-10) cc_final: 0.7175 (m-80) REVERT: M 94 ARG cc_start: 0.8119 (ptt90) cc_final: 0.7649 (ptt90) REVERT: M 100 ASP cc_start: 0.6815 (p0) cc_final: 0.6277 (p0) REVERT: N 34 ASP cc_start: 0.8314 (m-30) cc_final: 0.7728 (m-30) REVERT: N 39 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: O 6 GLN cc_start: 0.7974 (pm20) cc_final: 0.7471 (pm20) REVERT: O 10 GLU cc_start: 0.7129 (mp0) cc_final: 0.6889 (mp0) REVERT: O 47 TRP cc_start: 0.8446 (t-100) cc_final: 0.8155 (t60) REVERT: O 59 TYR cc_start: 0.8384 (m-80) cc_final: 0.8128 (m-80) REVERT: O 90 TYR cc_start: 0.7487 (m-80) cc_final: 0.7274 (m-80) REVERT: O 100 ARG cc_start: 0.8352 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: O 100 TYR cc_start: 0.8180 (m-80) cc_final: 0.7915 (m-80) REVERT: P 34 ASP cc_start: 0.8543 (m-30) cc_final: 0.8135 (m-30) outliers start: 55 outliers final: 42 residues processed: 374 average time/residue: 0.1858 time to fit residues: 111.6521 Evaluate side-chains 355 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 310 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 313 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 308 optimal weight: 0.0040 chunk 136 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101993 restraints weight = 52737.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105657 restraints weight = 26239.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108107 restraints weight = 16442.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109677 restraints weight = 11955.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110662 restraints weight = 9672.028| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 30737 Z= 0.116 Angle : 0.593 14.635 41936 Z= 0.300 Chirality : 0.044 0.308 4828 Planarity : 0.004 0.044 5346 Dihedral : 5.558 54.756 5085 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.69 % Allowed : 16.78 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.24 (0.14), residues: 3747 helix: 2.25 (0.21), residues: 672 sheet: 0.54 (0.17), residues: 903 loop : -0.70 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 357 TYR 0.028 0.001 TYR H 79 PHE 0.020 0.001 PHE N 95C TRP 0.044 0.001 TRP M 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00266 (30645) covalent geometry : angle 0.56152 (41706) SS BOND : bond 0.00253 ( 46) SS BOND : angle 2.59694 ( 92) hydrogen bonds : bond 0.03553 ( 1136) hydrogen bonds : angle 5.43328 ( 3081) link_ALPHA1-6 : bond 0.00676 ( 1) link_ALPHA1-6 : angle 1.32124 ( 3) link_BETA1-4 : bond 0.00935 ( 10) link_BETA1-4 : angle 2.79332 ( 30) link_BETA1-6 : bond 0.00328 ( 3) link_BETA1-6 : angle 1.41583 ( 9) link_NAG-ASN : bond 0.00336 ( 32) link_NAG-ASN : angle 2.73672 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7494 Ramachandran restraints generated. 3747 Oldfield, 0 Emsley, 3747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 336 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 316 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8505 (p) REVERT: A 317 ASN cc_start: 0.8733 (m-40) cc_final: 0.8490 (m110) REVERT: A 405 ASP cc_start: 0.8370 (m-30) cc_final: 0.8083 (m-30) REVERT: A 471 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7716 (mm-30) REVERT: B 102 ARG cc_start: 0.7323 (mmp80) cc_final: 0.6851 (mmp80) REVERT: B 405 ASP cc_start: 0.8290 (m-30) cc_final: 0.8060 (m-30) REVERT: B 467 ASP cc_start: 0.7268 (p0) cc_final: 0.6893 (p0) REVERT: B 664 ILE cc_start: 0.8367 (mm) cc_final: 0.8023 (mm) REVERT: B 755 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: B 1083 HIS cc_start: 0.7960 (t70) cc_final: 0.7635 (t70) REVERT: E 52 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8416 (tm-30) REVERT: E 405 ASP cc_start: 0.8366 (m-30) cc_final: 0.7923 (m-30) REVERT: E 462 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8413 (mmmt) REVERT: E 578 ASP cc_start: 0.8078 (t70) cc_final: 0.7873 (t0) REVERT: E 664 ILE cc_start: 0.8322 (mm) cc_final: 0.8002 (mm) REVERT: E 697 MET cc_start: 0.8212 (ptm) cc_final: 0.7976 (ttp) REVERT: E 1135 ASN cc_start: 0.8513 (t0) cc_final: 0.8177 (t0) REVERT: H 32 TYR cc_start: 0.8107 (m-80) cc_final: 0.7895 (m-80) REVERT: H 59 TYR cc_start: 0.8548 (m-80) cc_final: 0.8152 (m-80) REVERT: H 94 ARG cc_start: 0.7632 (ptt90) cc_final: 0.7210 (ptt90) REVERT: L 34 ASP cc_start: 0.8389 (m-30) cc_final: 0.7754 (m-30) REVERT: L 86 TYR cc_start: 0.7301 (m-10) cc_final: 0.7082 (m-80) REVERT: M 100 ASP cc_start: 0.7517 (p0) cc_final: 0.7245 (p0) REVERT: N 34 ASP cc_start: 0.8277 (m-30) cc_final: 0.7606 (m-30) REVERT: N 39 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8318 (mmm-85) REVERT: O 6 GLN cc_start: 0.7955 (pm20) cc_final: 0.7430 (pm20) REVERT: O 10 GLU cc_start: 0.7113 (mp0) cc_final: 0.6809 (mp0) REVERT: O 47 TRP cc_start: 0.8409 (t-100) cc_final: 0.8149 (t60) REVERT: O 59 TYR cc_start: 0.8345 (m-80) cc_final: 0.8075 (m-80) REVERT: P 34 ASP cc_start: 0.8486 (m-30) cc_final: 0.8039 (m-30) outliers start: 48 outliers final: 38 residues processed: 376 average time/residue: 0.1847 time to fit residues: 111.7902 Evaluate side-chains 366 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 869 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 1040 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain P residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 320 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 348 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 301 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094611 restraints weight = 54007.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.097817 restraints weight = 28377.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099952 restraints weight = 18434.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101386 restraints weight = 13738.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102295 restraints weight = 11288.075| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30737 Z= 0.273 Angle : 0.711 15.838 41936 Z= 0.359 Chirality : 0.048 0.333 4828 Planarity : 0.005 0.046 5346 Dihedral : 5.980 58.758 5085 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.62 % Allowed : 17.06 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.09 (0.14), residues: 3747 helix: 1.94 (0.20), residues: 675 sheet: 0.43 (0.16), residues: 900 loop : -0.96 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.035 0.002 TYR H 32 PHE 0.019 0.002 PHE A 238 TRP 0.061 0.002 TRP M 47 HIS 0.007 0.002 HIS E1048 Details of bonding type rmsd covalent geometry : bond 0.00643 (30645) covalent geometry : angle 0.67931 (41706) SS BOND : bond 0.00429 ( 46) SS BOND : angle 2.81286 ( 92) hydrogen bonds : bond 0.04322 ( 1136) hydrogen bonds : angle 5.77298 ( 3081) link_ALPHA1-6 : bond 0.00753 ( 1) link_ALPHA1-6 : angle 1.74528 ( 3) link_BETA1-4 : bond 0.00956 ( 10) link_BETA1-4 : angle 3.03788 ( 30) link_BETA1-6 : bond 0.00167 ( 3) link_BETA1-6 : angle 1.75757 ( 9) link_NAG-ASN : bond 0.00384 ( 32) link_NAG-ASN : angle 3.03213 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5990.74 seconds wall clock time: 103 minutes 50.65 seconds (6230.65 seconds total)