Starting phenix.real_space_refine on Sun Feb 8 09:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958.map" model { file = "/net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x25_32958/02_2026/7x25_32958_neut.cif" } resolution = 2.49 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8700 atoms to isotropic. 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 183 5.16 5 C 23480 2.51 5 N 6191 2.21 5 O 7256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37110 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "C" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 213, 1573 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1599 Chain: "F" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9189 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 215, 1582 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 215, 1582 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1611 Chain: "I" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 9189 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 9132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9132 Classifications: {'peptide': 1181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 58, 'TRANS': 1120} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 8.22, per 1000 atoms: 0.22 Number of scatterers: 37110 At special positions: 0 Unit cell: (153.715, 199.18, 240.315, 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 183 16.00 O 7256 8.00 N 6191 7.00 C 23480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 176 " - pdb=" SG CYS G 214 " distance=2.03 Simple disulfide: pdb=" SG CYS G 185 " - pdb=" SG CYS G 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 339 " - pdb=" SG CYS G 349 " distance=2.03 Simple disulfide: pdb=" SG CYS G 383 " - pdb=" SG CYS G 407 " distance=2.01 Simple disulfide: pdb=" SG CYS G 425 " - pdb=" SG CYS G 478 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 585 " distance=2.02 Simple disulfide: pdb=" SG CYS G 503 " - pdb=" SG CYS G 526 " distance=2.03 Simple disulfide: pdb=" SG CYS G 603 " - pdb=" SG CYS G 654 " distance=2.03 Simple disulfide: pdb=" SG CYS G 620 " - pdb=" SG CYS G 650 " distance=2.03 Simple disulfide: pdb=" SG CYS G 727 " - pdb=" SG CYS G 736 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.03 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 214 " distance=2.03 Simple disulfide: pdb=" SG CYS I 185 " - pdb=" SG CYS I 237 " distance=2.03 Simple disulfide: pdb=" SG CYS I 339 " - pdb=" SG CYS I 349 " distance=2.03 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 407 " distance=2.02 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 585 " distance=2.08 Simple disulfide: pdb=" SG CYS I 503 " - pdb=" SG CYS I 526 " distance=2.02 Simple disulfide: pdb=" SG CYS I 603 " - pdb=" SG CYS I 654 " distance=2.03 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.02 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.03 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.03 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1106 " - pdb=" SG CYS I1117 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.03 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.03 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.03 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.03 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.01 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.03 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.03 Simple disulfide: pdb=" SG CYS J 806 " - pdb=" SG CYS J 828 " distance=2.03 Simple disulfide: pdb=" SG CYS J 811 " - pdb=" SG CYS J 817 " distance=2.03 Simple disulfide: pdb=" SG CYS J 912 " - pdb=" SG CYS J 925 " distance=2.03 Simple disulfide: pdb=" SG CYS J1106 " - pdb=" SG CYS J1117 " distance=2.03 Simple disulfide: pdb=" SG CYS J1156 " - pdb=" SG CYS J1164 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.7 seconds 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8978 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 86 sheets defined 18.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.652A pdb=" N SER C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP E 90 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 removed outlier: 4.096A pdb=" N PHE G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 222 through 232 removed outlier: 4.006A pdb=" N TYR G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER G 390 " --> pdb=" O PRO G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 399 Processing helix chain 'G' and resid 411 through 416 Processing helix chain 'G' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER G 435 " --> pdb=" O ALA G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET G 452 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 528 removed outlier: 4.047A pdb=" N SER G 528 " --> pdb=" O PRO G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 591 through 595 Processing helix chain 'G' and resid 805 through 812 Processing helix chain 'G' and resid 814 through 823 removed outlier: 3.616A pdb=" N GLN G 819 " --> pdb=" O GLN G 815 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU G 820 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU G 823 " --> pdb=" O GLN G 819 " (cutoff:3.500A) Processing helix chain 'G' and resid 826 through 854 removed outlier: 3.600A pdb=" N LYS G 830 " --> pdb=" O GLN G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 915 removed outlier: 3.711A pdb=" N CYS G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET G 913 " --> pdb=" O TYR G 909 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN G 914 " --> pdb=" O ASP G 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 926 through 931 Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1012 removed outlier: 4.472A pdb=" N PHE G1012 " --> pdb=" O GLN G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1039 removed outlier: 3.601A pdb=" N LEU G1036 " --> pdb=" O ALA G1032 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1056 removed outlier: 3.722A pdb=" N GLN G1056 " --> pdb=" O GLY G1052 " (cutoff:3.500A) Processing helix chain 'G' and resid 1059 through 1107 removed outlier: 3.991A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G1094 " --> pdb=" O GLU G1090 " (cutoff:3.500A) Processing helix chain 'G' and resid 1219 through 1223 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.692A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 36 through 41 removed outlier: 4.101A pdb=" N PHE I 40 " --> pdb=" O GLN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 222 through 232 removed outlier: 4.065A pdb=" N TYR I 231 " --> pdb=" O SER I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 399 Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER I 435 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 529 removed outlier: 4.048A pdb=" N SER I 528 " --> pdb=" O PRO I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 805 through 812 Processing helix chain 'I' and resid 814 through 823 removed outlier: 3.791A pdb=" N GLU I 823 " --> pdb=" O GLN I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 826 through 854 removed outlier: 3.564A pdb=" N LYS I 830 " --> pdb=" O GLN I 826 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 915 removed outlier: 3.603A pdb=" N CYS I 912 " --> pdb=" O GLY I 908 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN I 914 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 940 through 954 removed outlier: 3.627A pdb=" N SER I 954 " --> pdb=" O SER I 950 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1012 removed outlier: 4.413A pdb=" N PHE I1012 " --> pdb=" O GLN I1009 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 removed outlier: 3.597A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1056 removed outlier: 3.821A pdb=" N GLN I1056 " --> pdb=" O GLY I1052 " (cutoff:3.500A) Processing helix chain 'I' and resid 1059 through 1107 removed outlier: 3.981A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU I1094 " --> pdb=" O GLU I1090 " (cutoff:3.500A) Processing helix chain 'I' and resid 1219 through 1223 Processing helix chain 'J' and resid 36 through 41 removed outlier: 4.066A pdb=" N PHE J 40 " --> pdb=" O GLN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 222 through 232 removed outlier: 4.027A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 Processing helix chain 'J' and resid 411 through 416 Processing helix chain 'J' and resid 431 through 435 removed outlier: 3.704A pdb=" N SER J 435 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 453 removed outlier: 3.636A pdb=" N MET J 452 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 524 through 529 removed outlier: 3.735A pdb=" N SER J 528 " --> pdb=" O PRO J 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 805 through 812 Processing helix chain 'J' and resid 814 through 823 removed outlier: 3.822A pdb=" N GLU J 823 " --> pdb=" O GLN J 819 " (cutoff:3.500A) Processing helix chain 'J' and resid 826 through 854 removed outlier: 3.654A pdb=" N LYS J 830 " --> pdb=" O GLN J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 888 through 898 Processing helix chain 'J' and resid 907 through 915 removed outlier: 3.936A pdb=" N GLN J 914 " --> pdb=" O ASP J 910 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 931 Processing helix chain 'J' and resid 940 through 953 Processing helix chain 'J' and resid 971 through 982 Processing helix chain 'J' and resid 986 through 993 Processing helix chain 'J' and resid 993 through 1007 Processing helix chain 'J' and resid 1008 through 1012 removed outlier: 4.467A pdb=" N PHE J1012 " --> pdb=" O GLN J1009 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1039 removed outlier: 3.630A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1050 through 1056 removed outlier: 3.670A pdb=" N GLN J1056 " --> pdb=" O GLY J1052 " (cutoff:3.500A) Processing helix chain 'J' and resid 1059 through 1107 removed outlier: 3.937A pdb=" N ALA J1065 " --> pdb=" O PRO J1061 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU J1094 " --> pdb=" O GLU J1090 " (cutoff:3.500A) Processing helix chain 'J' and resid 1219 through 1223 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR A 94 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 152 removed outlier: 4.637A pdb=" N LEU A 148 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER A 187 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 150 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU A 185 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 152 " --> pdb=" O TYR A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 13 removed outlier: 5.678A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER C 163 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR E 94 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AB6, first strand: chain 'E' and resid 148 through 152 removed outlier: 4.637A pdb=" N LEU E 148 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER E 187 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS E 150 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU E 185 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR E 152 " --> pdb=" O TYR E 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 160 Processing sheet with id=AB8, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AB9, first strand: chain 'F' and resid 11 through 13 removed outlier: 5.677A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER F 163 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.431A pdb=" N HIS G 91 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 67 through 75 removed outlier: 4.302A pdb=" N ARG G 335 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.531A pdb=" N TYR G 314 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL G 263 " --> pdb=" O THR G 283 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR G 283 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 265 " --> pdb=" O PHE G 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 88 through 89 removed outlier: 7.322A pdb=" N SER G 88 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR G 206 " --> pdb=" O SER G 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 110 through 111 Processing sheet with id=AD1, first strand: chain 'G' and resid 127 through 129 removed outlier: 3.880A pdb=" N ALA G 309 " --> pdb=" O THR G 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 153 through 155 Processing sheet with id=AD3, first strand: chain 'G' and resid 689 through 690 removed outlier: 5.499A pdb=" N VAL G 360 " --> pdb=" O TYR G 663 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR G 663 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER G 362 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL G 661 " --> pdb=" O SER G 362 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER G 364 " --> pdb=" O VAL G 659 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL G 659 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS G 713 " --> pdb=" O PHE G 674 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 373 through 376 removed outlier: 4.615A pdb=" N VAL G 639 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 631 " --> pdb=" O VAL G 639 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS G 400 " --> pdb=" O TYR G 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 445 " --> pdb=" O LYS G 400 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 407 through 409 removed outlier: 6.704A pdb=" N CYS G 407 " --> pdb=" O CYS G 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 513 through 515 removed outlier: 3.699A pdb=" N TYR G 497 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER G 557 " --> pdb=" O ASN G 501 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 717 through 724 removed outlier: 6.738A pdb=" N VAL G 718 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N SER G 761 " --> pdb=" O VAL G 718 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N SER G 720 " --> pdb=" O SER G 761 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 768 through 769 removed outlier: 5.798A pdb=" N ILE G 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.073A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY G1188 " --> pdb=" O ALA G1193 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G1193 " --> pdb=" O GLY G1188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 1121 through 1130 removed outlier: 6.073A pdb=" N HIS G1122 " --> pdb=" O TYR G1141 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR G1141 " --> pdb=" O HIS G1122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS G 779 " --> pdb=" O ALA I 969 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AE4, first strand: chain 'G' and resid 857 through 858 Processing sheet with id=AE5, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.302A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL J1124 " --> pdb=" O VAL J1139 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR J1141 " --> pdb=" O HIS J1122 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS J1122 " --> pdb=" O TYR J1141 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 967 through 969 removed outlier: 4.302A pdb=" N LYS J 779 " --> pdb=" O ALA G 969 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR J 777 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA J1152 " --> pdb=" O TYR J 777 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS J 779 " --> pdb=" O VAL J1150 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL J1150 " --> pdb=" O LYS J 779 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER J 781 " --> pdb=" O GLU J1148 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU J1148 " --> pdb=" O SER J 781 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS J1146 " --> pdb=" O PRO J 783 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL J1150 " --> pdb=" O LYS J1174 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE J1172 " --> pdb=" O ALA J1152 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY J1188 " --> pdb=" O ALA J1193 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA J1193 " --> pdb=" O GLY J1188 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.645A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AF1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AF2, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.636A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 152 " --> pdb=" O TYR H 183 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AF4, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.413A pdb=" N HIS I 91 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 67 through 75 removed outlier: 4.234A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.312A pdb=" N VAL I 263 " --> pdb=" O THR I 283 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR I 283 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU I 265 " --> pdb=" O PHE I 281 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 110 through 111 Processing sheet with id=AF8, first strand: chain 'I' and resid 127 through 129 removed outlier: 3.718A pdb=" N ALA I 309 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 153 through 155 Processing sheet with id=AG1, first strand: chain 'I' and resid 206 through 208 removed outlier: 6.400A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'I' and resid 689 through 690 removed outlier: 4.542A pdb=" N VAL I 659 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER I 365 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL I 657 " --> pdb=" O SER I 365 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS I 713 " --> pdb=" O PHE I 674 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 372 through 376 removed outlier: 6.766A pdb=" N GLY I 372 " --> pdb=" O GLU I 605 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N SER I 607 " --> pdb=" O GLY I 372 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL I 374 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 631 " --> pdb=" O VAL I 639 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS I 400 " --> pdb=" O TYR I 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR I 445 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 407 through 409 Processing sheet with id=AG6, first strand: chain 'I' and resid 513 through 515 removed outlier: 3.700A pdb=" N TYR I 497 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER I 557 " --> pdb=" O ASN I 501 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 717 through 724 removed outlier: 6.707A pdb=" N VAL I 718 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N SER I 761 " --> pdb=" O VAL I 718 " (cutoff:3.500A) removed outlier: 9.948A pdb=" N SER I 720 " --> pdb=" O SER I 761 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU I 735 " --> pdb=" O LEU I 731 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 768 through 769 removed outlier: 5.811A pdb=" N ILE I 768 " --> pdb=" O SER J 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 1121 through 1130 removed outlier: 6.063A pdb=" N HIS I1122 " --> pdb=" O TYR I1141 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR I1141 " --> pdb=" O HIS I1122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS I1146 " --> pdb=" O PRO I 783 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU I1148 " --> pdb=" O SER I 781 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER I 781 " --> pdb=" O GLU I1148 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL I1150 " --> pdb=" O LYS I 779 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS I 779 " --> pdb=" O VAL I1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA I1152 " --> pdb=" O TYR I 777 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR I 777 " --> pdb=" O ALA I1152 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS I 779 " --> pdb=" O ALA J 969 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AH3, first strand: chain 'I' and resid 1202 through 1205 removed outlier: 4.150A pdb=" N CYS I1164 " --> pdb=" O VAL I1205 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AH5, first strand: chain 'J' and resid 67 through 75 removed outlier: 4.296A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.528A pdb=" N TYR J 314 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL J 263 " --> pdb=" O THR J 283 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR J 283 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU J 265 " --> pdb=" O PHE J 281 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.291A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'J' and resid 110 through 111 Processing sheet with id=AH9, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.828A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 153 through 155 Processing sheet with id=AI2, first strand: chain 'J' and resid 689 through 690 removed outlier: 4.596A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 372 through 376 removed outlier: 3.906A pdb=" N GLY J 372 " --> pdb=" O CYS J 603 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.755A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 445 " --> pdb=" O LYS J 400 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 408 through 409 Processing sheet with id=AI6, first strand: chain 'J' and resid 497 through 503 removed outlier: 3.701A pdb=" N TYR J 497 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER J 557 " --> pdb=" O ASN J 501 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 717 through 724 removed outlier: 6.728A pdb=" N VAL J 718 " --> pdb=" O LEU J 759 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N SER J 761 " --> pdb=" O VAL J 718 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N SER J 720 " --> pdb=" O SER J 761 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 802 through 804 Processing sheet with id=AI9, first strand: chain 'J' and resid 1202 through 1205 removed outlier: 4.167A pdb=" N CYS J1164 " --> pdb=" O VAL J1205 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.676A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.796A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AJ4, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 154 through 155 1266 hydrogen bonds defined for protein. 3211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.65 Time building geometry restraints manager: 3.92 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: 10725 1.33 - 1.46: 9041 1.46 - 1.59: 17960 1.59 - 1.71: 0 1.71 - 1.84: 240 Bond restraints: 37966 Sorted by residual: bond pdb=" C SER E 186 " pdb=" O SER E 186 " ideal model delta sigma weight residual 1.236 1.363 -0.127 1.21e-02 6.83e+03 1.11e+02 bond pdb=" C SER A 186 " pdb=" O SER A 186 " ideal model delta sigma weight residual 1.236 1.363 -0.127 1.21e-02 6.83e+03 1.10e+02 bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.21e-02 6.83e+03 1.09e+02 bond pdb=" C SER E 160 " pdb=" O SER E 160 " ideal model delta sigma weight residual 1.234 1.359 -0.124 1.22e-02 6.72e+03 1.04e+02 bond pdb=" C SER A 160 " pdb=" O SER A 160 " ideal model delta sigma weight residual 1.234 1.358 -0.124 1.22e-02 6.72e+03 1.03e+02 ... (remaining 37961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 51040 3.47 - 6.94: 571 6.94 - 10.41: 32 10.41 - 13.88: 26 13.88 - 17.35: 1 Bond angle restraints: 51670 Sorted by residual: angle pdb=" O SER A 186 " pdb=" C SER A 186 " pdb=" CA ASER A 186 " ideal model delta sigma weight residual 120.38 132.23 -11.85 1.09e+00 8.42e-01 1.18e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.21 -11.83 1.09e+00 8.42e-01 1.18e+02 angle pdb=" O SER E 186 " pdb=" C SER E 186 " pdb=" CA ASER E 186 " ideal model delta sigma weight residual 120.38 132.18 -11.80 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER A 186 " pdb=" C SER A 186 " pdb=" CA BSER A 186 " ideal model delta sigma weight residual 120.38 132.18 -11.80 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.17 -11.79 1.09e+00 8.42e-01 1.17e+02 ... (remaining 51665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19808 18.00 - 35.99: 2081 35.99 - 53.99: 621 53.99 - 71.98: 154 71.98 - 89.98: 72 Dihedral angle restraints: 22736 sinusoidal: 8667 harmonic: 14069 Sorted by residual: dihedral pdb=" CA GLY G 380 " pdb=" C GLY G 380 " pdb=" N VAL G 381 " pdb=" CA VAL G 381 " ideal model delta harmonic sigma weight residual -180.00 -137.64 -42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CB CYS I 176 " pdb=" SG CYS I 176 " pdb=" SG CYS I 214 " pdb=" CB CYS I 214 " ideal model delta sinusoidal sigma weight residual -86.00 -160.84 74.84 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CA GLU A 155 " pdb=" C GLU A 155 " pdb=" N PRO A 156 " pdb=" CA PRO A 156 " ideal model delta harmonic sigma weight residual 0.00 41.03 -41.03 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 22733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4816 0.084 - 0.168: 835 0.168 - 0.251: 146 0.251 - 0.335: 8 0.335 - 0.419: 8 Chirality restraints: 5813 Sorted by residual: chirality pdb=" CA GLN H 199 " pdb=" N GLN H 199 " pdb=" C GLN H 199 " pdb=" CB GLN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA ALA E 24 " pdb=" N ALA E 24 " pdb=" C ALA E 24 " pdb=" CB ALA E 24 " both_signs ideal model delta sigma weight residual False 2.48 2.85 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA BSER E 186 " pdb=" N SER E 186 " pdb=" C SER E 186 " pdb=" CB BSER E 186 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 5810 not shown) Planarity restraints: 6698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 22 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C CYS E 22 " 0.079 2.00e-02 2.50e+03 pdb=" O CYS E 22 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS E 23 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 377 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN I 377 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN I 377 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA I 378 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN K 91 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C GLN K 91 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN K 91 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 92 " 0.015 2.00e-02 2.50e+03 ... (remaining 6695 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 4 1.82 - 2.59: 319 2.59 - 3.36: 45305 3.36 - 4.13: 89421 4.13 - 4.90: 161714 Nonbonded interactions: 296763 Sorted by model distance: nonbonded pdb=" OE2 GLU I 376 " pdb=" NZ LYS I 595 " model vdw 1.050 3.120 nonbonded pdb=" OD2 ASP I 580 " pdb=" NH2 ARG J 62 " model vdw 1.593 3.120 nonbonded pdb=" O SER E 75 " pdb=" OG SER H 168 " model vdw 1.655 3.040 nonbonded pdb=" SG CYS I 437 " pdb=" CA GLY I 610 " model vdw 1.700 3.800 nonbonded pdb=" O SER E 75 " pdb=" CB SER H 168 " model vdw 2.037 3.440 ... (remaining 296758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 25 or resid 32 through 159 or resid 167 through \ 185 or resid 187 through 221)) selection = (chain 'E' and (resid 3 through 159 or resid 167 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 3 through 25 or resid 32 through 159 or resid 167 through \ 185 or resid 187 through 221)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'K' } ncs_group { reference = (chain 'G' and (resid 18 through 507 or resid 516 through 1223)) selection = (chain 'I' and (resid 18 through 507 or resid 516 through 1223)) selection = chain 'J' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.140 Find NCS groups from input model: 0.760 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: 0.010 Load rotamer database and sin/cos tables:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3139 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 : 0.008 0.127 38026 Z= 0.537 Angle : 1.079 17.351 51790 Z= 0.722 Chirality : 0.065 0.419 5813 Planarity : 0.005 0.058 6698 Dihedral : 17.292 89.977 13578 Min Nonbonded Distance : 1.050 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.40 % Favored : 88.58 % Rotamer: Outliers : 9.22 % Allowed : 16.93 % Favored : 73.85 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.13 % Twisted Proline : 1.21 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4813 helix: 1.08 (0.21), residues: 683 sheet: -1.21 (0.14), residues: 1331 loop : -2.06 (0.11), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 235 TYR 0.031 0.002 TYR J 438 PHE 0.022 0.002 PHE G 156 TRP 0.013 0.001 TRP C 36 HIS 0.007 0.001 HIS G 194 Details of bonding type rmsd covalent geometry : bond 0.00766 (37966) covalent geometry : angle 1.07859 (51670) SS BOND : bond 0.00929 ( 60) SS BOND : angle 1.40838 ( 120) hydrogen bonds : bond 0.18203 ( 1237) hydrogen bonds : angle 7.63102 ( 3211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 381 poor density : 699 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 214 VAL cc_start: 0.5733 (t) cc_final: 0.5457 (t) REVERT: F 39 GLN cc_start: 0.1644 (pt0) cc_final: 0.1202 (tm-30) REVERT: G 25 SER cc_start: -0.2115 (OUTLIER) cc_final: -0.2478 (t) REVERT: G 102 VAL cc_start: 0.0841 (OUTLIER) cc_final: 0.0633 (m) REVERT: G 294 SER cc_start: 0.2380 (OUTLIER) cc_final: 0.0446 (m) REVERT: G 871 LEU cc_start: 0.1244 (OUTLIER) cc_final: 0.0831 (pp) REVERT: G 1175 THR cc_start: 0.0480 (OUTLIER) cc_final: -0.1352 (t) REVERT: I 704 TYR cc_start: 0.2606 (OUTLIER) cc_final: 0.2317 (p90) REVERT: I 910 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5078 (m-30) REVERT: J 228 PHE cc_start: 0.4833 (t80) cc_final: 0.4322 (t80) REVERT: J 256 ILE cc_start: 0.7865 (tt) cc_final: 0.7641 (pp) REVERT: J 361 TYR cc_start: 0.6122 (m-80) cc_final: 0.5813 (m-80) REVERT: J 373 SER cc_start: 0.1379 (OUTLIER) cc_final: 0.1107 (t) REVERT: J 856 SER cc_start: -0.1851 (OUTLIER) cc_final: -0.2634 (p) REVERT: J 910 ASP cc_start: 0.1049 (OUTLIER) cc_final: 0.0650 (p0) REVERT: J 1209 VAL cc_start: 0.2272 (OUTLIER) cc_final: 0.1759 (m) REVERT: K 198 THR cc_start: 0.4104 (OUTLIER) cc_final: 0.3668 (p) outliers start: 381 outliers final: 58 residues processed: 1020 average time/residue: 0.5264 time to fit residues: 693.2534 Evaluate side-chains 462 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 392 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 43 GLN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 294 SER Chi-restraints excluded: chain G residue 330 ASP Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 422 ASP Chi-restraints excluded: chain G residue 604 VAL Chi-restraints excluded: chain G residue 621 THR Chi-restraints excluded: chain G residue 781 SER Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 874 LEU Chi-restraints excluded: chain G residue 893 LEU Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1095 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain G residue 1203 LYS Chi-restraints excluded: chain G residue 1216 THR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 704 TYR Chi-restraints excluded: chain I residue 720 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 910 ASP Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1089 SER Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 704 TYR Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 829 SER Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 890 ILE Chi-restraints excluded: chain J residue 910 ASP Chi-restraints excluded: chain J residue 1089 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1216 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 470 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 162 ASN A 178 GLN C 39 GLN C 43 GLN E 6 GLN E 178 GLN F 101 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN G 348 HIS G 521 ASN G 592 ASN G 599 GLN G 681 HIS G 819 GLN G1009 GLN ** G1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1146 HIS H 199 GLN I 114 ASN I 208 HIS I 244 ASN I 377 GLN ** I 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 981 ASN I1023 GLN I1056 GLN ** I1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN J 521 ASN J 628 GLN J 681 HIS ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 812 ASN J 819 GLN J 836 HIS J1020 GLN J1129 ASN J1132 ASN J1146 HIS J1213 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.195819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.174482 restraints weight = 189812.968| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 5.13 r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 38026 Z= 0.359 Angle : 1.048 15.959 51790 Z= 0.558 Chirality : 0.057 0.345 5813 Planarity : 0.007 0.094 6698 Dihedral : 7.616 67.864 5352 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.01 % Favored : 91.74 % Rotamer: Outliers : 7.67 % Allowed : 21.19 % Favored : 71.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.11), residues: 4813 helix: -0.38 (0.18), residues: 726 sheet: -1.07 (0.14), residues: 1343 loop : -2.23 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 235 TYR 0.041 0.003 TYR C 92 PHE 0.047 0.004 PHE E 129 TRP 0.083 0.004 TRP E 47 HIS 0.023 0.003 HIS G 670 Details of bonding type rmsd covalent geometry : bond 0.00721 (37966) covalent geometry : angle 1.04422 (51670) SS BOND : bond 0.02179 ( 60) SS BOND : angle 2.12938 ( 120) hydrogen bonds : bond 0.06137 ( 1237) hydrogen bonds : angle 6.99061 ( 3211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 432 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7335 (ttm) cc_final: 0.7078 (tpt) REVERT: C 92 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.5383 (p90) REVERT: E 59 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7435 (ttm110) REVERT: G 31 ILE cc_start: -0.0105 (OUTLIER) cc_final: -0.0862 (pp) REVERT: G 49 ASP cc_start: 0.5779 (t0) cc_final: 0.5493 (t0) REVERT: G 442 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8531 (pp) REVERT: G 452 MET cc_start: 0.8683 (pmm) cc_final: 0.8245 (pmm) REVERT: G 523 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.4556 (m-80) REVERT: G 1090 GLU cc_start: 0.7722 (tp30) cc_final: 0.7377 (tp30) REVERT: G 1137 MET cc_start: -0.1168 (ptp) cc_final: -0.2410 (ptp) REVERT: H 183 TYR cc_start: 0.4741 (p90) cc_final: 0.4178 (p90) REVERT: I 132 ILE cc_start: 0.3801 (OUTLIER) cc_final: 0.3397 (mp) REVERT: I 203 SER cc_start: 0.0873 (OUTLIER) cc_final: 0.0523 (p) REVERT: I 234 LEU cc_start: 0.5118 (OUTLIER) cc_final: 0.4828 (mm) REVERT: I 295 ILE cc_start: 0.1970 (OUTLIER) cc_final: 0.1745 (mp) REVERT: I 310 TRP cc_start: 0.6787 (m100) cc_final: 0.6038 (m-10) REVERT: I 717 LEU cc_start: 0.3324 (OUTLIER) cc_final: 0.3057 (tm) REVERT: J 96 THR cc_start: 0.8311 (m) cc_final: 0.8063 (t) REVERT: J 110 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: J 233 ASN cc_start: 0.5996 (m-40) cc_final: 0.5777 (m110) REVERT: J 464 ILE cc_start: 0.9443 (mp) cc_final: 0.9203 (mt) REVERT: J 469 TYR cc_start: 0.6589 (t80) cc_final: 0.6202 (t80) REVERT: J 709 THR cc_start: 0.5349 (p) cc_final: 0.4592 (p) REVERT: J 710 PRO cc_start: 0.4214 (Cg_exo) cc_final: 0.3383 (Cg_endo) REVERT: J 816 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7724 (tppp) REVERT: J 943 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5262 (tmt) REVERT: J 1008 MET cc_start: 0.4804 (mmp) cc_final: 0.3934 (mmm) REVERT: J 1105 GLU cc_start: 0.3011 (OUTLIER) cc_final: 0.2744 (mt-10) REVERT: J 1146 HIS cc_start: 0.3619 (OUTLIER) cc_final: 0.2829 (m-70) outliers start: 317 outliers final: 104 residues processed: 682 average time/residue: 0.5324 time to fit residues: 466.9315 Evaluate side-chains 431 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 312 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 374 VAL Chi-restraints excluded: chain G residue 442 ILE Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 500 ILE Chi-restraints excluded: chain G residue 523 TYR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 604 VAL Chi-restraints excluded: chain G residue 661 VAL Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1053 ASP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1125 SER Chi-restraints excluded: chain G residue 1173 ILE Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 132 ILE Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 608 LEU Chi-restraints excluded: chain I residue 616 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 687 SER Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 723 PHE Chi-restraints excluded: chain I residue 757 MET Chi-restraints excluded: chain I residue 761 SER Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 797 THR Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 856 SER Chi-restraints excluded: chain I residue 859 SER Chi-restraints excluded: chain I residue 934 VAL Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 890 ILE Chi-restraints excluded: chain J residue 899 THR Chi-restraints excluded: chain J residue 943 MET Chi-restraints excluded: chain J residue 1105 GLU Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 294 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 234 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 426 optimal weight: 1.9990 chunk 455 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 182 optimal weight: 0.3980 chunk 32 optimal weight: 0.0370 chunk 343 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN E 171 HIS ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 421 ASN G1009 GLN G1110 GLN I 395 GLN ** I 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 486 HIS ** I 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1072 ASN I1122 HIS I1129 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 566 GLN J 636 GLN J1016 ASN ** J1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1145 ASN J1212 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.195448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.170455 restraints weight = 203058.588| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 5.80 r_work: 0.4475 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38026 Z= 0.141 Angle : 0.721 11.836 51790 Z= 0.370 Chirality : 0.046 0.249 5813 Planarity : 0.005 0.046 6698 Dihedral : 5.798 50.081 5284 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.34 % Favored : 92.41 % Rotamer: Outliers : 4.72 % Allowed : 24.84 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.12), residues: 4813 helix: 0.58 (0.20), residues: 728 sheet: -0.86 (0.14), residues: 1311 loop : -2.03 (0.11), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 217 TYR 0.021 0.002 TYR J 241 PHE 0.024 0.002 PHE J 204 TRP 0.044 0.002 TRP E 47 HIS 0.015 0.001 HIS J1146 Details of bonding type rmsd covalent geometry : bond 0.00306 (37966) covalent geometry : angle 0.71861 (51670) SS BOND : bond 0.00334 ( 60) SS BOND : angle 1.44173 ( 120) hydrogen bonds : bond 0.04387 ( 1237) hydrogen bonds : angle 6.04299 ( 3211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 341 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7206 (tpt) REVERT: C 27 GLN cc_start: 0.5032 (pp30) cc_final: 0.4809 (pp30) REVERT: F 37 TYR cc_start: 0.5052 (m-80) cc_final: 0.4037 (t80) REVERT: G 31 ILE cc_start: -0.0585 (OUTLIER) cc_final: -0.1400 (pp) REVERT: G 49 ASP cc_start: 0.5983 (t0) cc_final: 0.5750 (t0) REVERT: G 334 ARG cc_start: 0.3750 (OUTLIER) cc_final: -0.0032 (ptm160) REVERT: G 395 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8826 (mm-40) REVERT: G 397 TYR cc_start: 0.7983 (p90) cc_final: 0.7288 (p90) REVERT: G 523 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.5653 (m-80) REVERT: G 731 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7925 (mt) REVERT: G 871 LEU cc_start: -0.0334 (OUTLIER) cc_final: -0.0667 (pp) REVERT: H 183 TYR cc_start: 0.4820 (p90) cc_final: 0.4342 (p90) REVERT: I 203 SER cc_start: 0.0930 (OUTLIER) cc_final: 0.0642 (p) REVERT: I 234 LEU cc_start: 0.5209 (OUTLIER) cc_final: 0.4882 (mm) REVERT: I 245 ILE cc_start: 0.8401 (mt) cc_final: 0.8095 (tt) REVERT: I 939 MET cc_start: 0.5620 (OUTLIER) cc_final: 0.4693 (mtm) REVERT: I 1123 ILE cc_start: 0.4119 (mt) cc_final: 0.3855 (tp) REVERT: J 96 THR cc_start: 0.8324 (m) cc_final: 0.8096 (t) REVERT: J 188 GLU cc_start: 0.5806 (mm-30) cc_final: 0.5576 (mm-30) REVERT: J 233 ASN cc_start: 0.6358 (m-40) cc_final: 0.6106 (m110) REVERT: J 291 LYS cc_start: 0.8100 (mppt) cc_final: 0.7899 (mppt) REVERT: J 455 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6635 (t70) REVERT: J 469 TYR cc_start: 0.6413 (t80) cc_final: 0.5963 (t80) REVERT: J 541 TYR cc_start: 0.7354 (m-10) cc_final: 0.6749 (m-80) REVERT: J 694 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7195 (mtp85) REVERT: J 816 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8559 (tppp) REVERT: J 943 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6261 (tmt) REVERT: J 965 SER cc_start: -0.1053 (OUTLIER) cc_final: -0.1578 (p) REVERT: J 1016 ASN cc_start: 0.4314 (OUTLIER) cc_final: 0.3986 (t0) REVERT: J 1103 VAL cc_start: 0.7102 (t) cc_final: 0.6808 (m) REVERT: J 1137 MET cc_start: 0.5153 (pmm) cc_final: 0.4914 (pmm) REVERT: K 155 LEU cc_start: 0.3811 (OUTLIER) cc_final: 0.3115 (mt) outliers start: 195 outliers final: 76 residues processed: 497 average time/residue: 0.4887 time to fit residues: 313.0851 Evaluate side-chains 385 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 293 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 216 ASP Chi-restraints excluded: chain G residue 334 ARG Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 421 ASN Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 523 TYR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 714 VAL Chi-restraints excluded: chain G residue 731 LEU Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 871 LEU Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1089 SER Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 709 THR Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 791 THR Chi-restraints excluded: chain I residue 845 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 939 MET Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1139 VAL Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 156 PHE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 455 ASP Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 816 LYS Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 943 MET Chi-restraints excluded: chain J residue 965 SER Chi-restraints excluded: chain J residue 1016 ASN Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 465 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 157 optimal weight: 0.0370 chunk 190 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 252 optimal weight: 9.9990 chunk 127 optimal weight: 40.0000 chunk 254 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 43 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN G 346 GLN ** G 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 999 ASN G1009 GLN G1020 GLN ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1028 ASN ** G1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1132 ASN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1145 ASN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN I 486 HIS I 566 GLN I1002 ASN I1056 GLN I1132 ASN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 398 ASN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 GLN ** J 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 981 ASN J 994 GLN ** J1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1145 ASN ** J1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1212 GLN J1217 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.180062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.149788 restraints weight = 228892.500| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 5.89 r_work: 0.4124 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.9448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.185 38026 Z= 0.318 Angle : 0.936 16.189 51790 Z= 0.493 Chirality : 0.054 0.343 5813 Planarity : 0.007 0.088 6698 Dihedral : 6.675 58.959 5276 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.15 % Favored : 90.54 % Rotamer: Outliers : 6.24 % Allowed : 24.07 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.11), residues: 4813 helix: -0.26 (0.19), residues: 728 sheet: -0.82 (0.14), residues: 1276 loop : -2.31 (0.10), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 979 TYR 0.042 0.003 TYR G 314 PHE 0.049 0.004 PHE J 778 TRP 0.043 0.004 TRP E 47 HIS 0.072 0.003 HIS E 171 Details of bonding type rmsd covalent geometry : bond 0.00712 (37966) covalent geometry : angle 0.93202 (51670) SS BOND : bond 0.00606 ( 60) SS BOND : angle 2.06017 ( 120) hydrogen bonds : bond 0.06468 ( 1237) hydrogen bonds : angle 6.95128 ( 3211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 384 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7110 (tpt) REVERT: C 43 GLN cc_start: 0.6842 (tm130) cc_final: 0.6545 (tm130) REVERT: C 91 GLN cc_start: 0.4774 (OUTLIER) cc_final: 0.4118 (tt0) REVERT: E 105 ASP cc_start: 0.8435 (p0) cc_final: 0.6328 (p0) REVERT: G 31 ILE cc_start: -0.0053 (OUTLIER) cc_final: -0.0951 (pp) REVERT: G 84 MET cc_start: 0.5713 (tmm) cc_final: 0.4824 (tpt) REVERT: G 183 PHE cc_start: 0.5536 (OUTLIER) cc_final: 0.4974 (p90) REVERT: G 333 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6279 (mt) REVERT: G 452 MET cc_start: 0.8810 (pmm) cc_final: 0.8600 (pmm) REVERT: G 563 MET cc_start: 0.6254 (tpt) cc_final: 0.5902 (tpt) REVERT: G 771 ASP cc_start: 0.5308 (OUTLIER) cc_final: 0.4492 (m-30) REVERT: G 913 MET cc_start: 0.8689 (tpt) cc_final: 0.8302 (tpp) REVERT: G 950 SER cc_start: 0.5175 (OUTLIER) cc_final: 0.4518 (p) REVERT: G 1101 ASP cc_start: 0.7341 (m-30) cc_final: 0.6999 (m-30) REVERT: G 1102 LYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6427 (ttmm) REVERT: H 38 ARG cc_start: 0.8402 (ptm160) cc_final: 0.8174 (ttm-80) REVERT: H 95 TYR cc_start: 0.8884 (m-80) cc_final: 0.8666 (m-80) REVERT: H 157 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (p) REVERT: I 184 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.6023 (m-10) REVERT: I 240 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.4994 (tpp) REVERT: I 302 SER cc_start: 0.3898 (OUTLIER) cc_final: 0.3421 (t) REVERT: I 376 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5422 (mt-10) REVERT: I 1000 LYS cc_start: 0.6145 (mttt) cc_final: 0.5803 (mtpp) REVERT: I 1010 THR cc_start: 0.7649 (OUTLIER) cc_final: 0.7433 (p) REVERT: I 1180 ILE cc_start: 0.1133 (OUTLIER) cc_final: 0.0363 (tt) REVERT: J 96 THR cc_start: 0.8512 (m) cc_final: 0.8169 (p) REVERT: J 165 PHE cc_start: 0.7425 (m-10) cc_final: 0.7225 (m-10) REVERT: J 185 CYS cc_start: 0.4798 (m) cc_final: 0.4391 (m) REVERT: J 188 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6619 (mm-30) REVERT: J 428 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7688 (tt) REVERT: J 569 MET cc_start: 0.6869 (mpp) cc_final: 0.6436 (mpm) REVERT: J 666 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: J 899 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8625 (p) REVERT: J 910 ASP cc_start: 0.6681 (m-30) cc_final: 0.6385 (m-30) REVERT: J 987 GLN cc_start: 0.3776 (OUTLIER) cc_final: 0.3486 (pm20) REVERT: J 1008 MET cc_start: 0.5809 (mmp) cc_final: 0.5208 (mmm) REVERT: K 27 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: K 119 PHE cc_start: 0.7343 (m-80) cc_final: 0.7103 (m-10) REVERT: K 155 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4012 (mt) outliers start: 258 outliers final: 98 residues processed: 590 average time/residue: 0.5276 time to fit residues: 395.9389 Evaluate side-chains 413 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 294 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 92 TYR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 314 TYR Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 424 THR Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 950 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1102 LYS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain I residue 246 THR Chi-restraints excluded: chain I residue 289 THR Chi-restraints excluded: chain I residue 302 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 376 GLU Chi-restraints excluded: chain I residue 422 ASP Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 438 TYR Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 489 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 590 PHE Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 803 THR Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 857 GLN Chi-restraints excluded: chain I residue 873 LEU Chi-restraints excluded: chain I residue 934 VAL Chi-restraints excluded: chain I residue 1010 THR Chi-restraints excluded: chain I residue 1038 SER Chi-restraints excluded: chain I residue 1123 ILE Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 666 GLU Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 872 THR Chi-restraints excluded: chain J residue 899 THR Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 987 GLN Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 211 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 39 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 197 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 424 optimal weight: 0.8980 chunk 309 optimal weight: 0.5980 chunk 416 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1009 GLN G1110 GLN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 104 ASN I 566 GLN I1002 ASN ** I1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 769 GLN J1029 ASN J1146 HIS J1163 ASN K 148 GLN K 153 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.180553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.152581 restraints weight = 173035.718| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 4.87 r_work: 0.4158 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4154 r_free = 0.4154 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.9697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38026 Z= 0.150 Angle : 0.724 12.685 51790 Z= 0.371 Chirality : 0.046 0.260 5813 Planarity : 0.005 0.049 6698 Dihedral : 5.758 52.136 5272 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.57 % Favored : 92.18 % Rotamer: Outliers : 3.85 % Allowed : 27.04 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 4813 helix: 0.48 (0.19), residues: 741 sheet: -0.67 (0.14), residues: 1310 loop : -2.10 (0.11), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 758 TYR 0.024 0.002 TYR J 184 PHE 0.022 0.002 PHE J 778 TRP 0.045 0.002 TRP E 47 HIS 0.031 0.001 HIS I 486 Details of bonding type rmsd covalent geometry : bond 0.00337 (37966) covalent geometry : angle 0.72173 (51670) SS BOND : bond 0.00364 ( 60) SS BOND : angle 1.49757 ( 120) hydrogen bonds : bond 0.04476 ( 1237) hydrogen bonds : angle 6.04906 ( 3211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 323 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.5532 (ttp80) cc_final: 0.5220 (pmt-80) REVERT: A 81 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6968 (tpt) REVERT: C 91 GLN cc_start: 0.4879 (tm130) cc_final: 0.4063 (tt0) REVERT: E 47 TRP cc_start: 0.7554 (t60) cc_final: 0.7333 (t60) REVERT: F 37 TYR cc_start: 0.5700 (m-80) cc_final: 0.5329 (m-80) REVERT: G 31 ILE cc_start: 0.0256 (OUTLIER) cc_final: -0.0747 (pp) REVERT: G 84 MET cc_start: 0.5844 (tmm) cc_final: 0.4941 (tpt) REVERT: G 535 TRP cc_start: 0.8932 (t-100) cc_final: 0.8591 (t60) REVERT: G 563 MET cc_start: 0.6700 (tpt) cc_final: 0.6368 (tpt) REVERT: G 569 MET cc_start: 0.8222 (tmt) cc_final: 0.8020 (tmt) REVERT: G 571 PHE cc_start: 0.9337 (m-80) cc_final: 0.8960 (m-80) REVERT: G 771 ASP cc_start: 0.4770 (OUTLIER) cc_final: 0.3909 (m-30) REVERT: G 913 MET cc_start: 0.8528 (tpt) cc_final: 0.8238 (tpp) REVERT: G 1101 ASP cc_start: 0.7238 (m-30) cc_final: 0.6929 (m-30) REVERT: H 29 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6961 (t80) REVERT: H 155 GLU cc_start: 0.5973 (pt0) cc_final: 0.5669 (mt-10) REVERT: I 287 TYR cc_start: 0.8222 (m-80) cc_final: 0.7983 (m-80) REVERT: I 906 MET cc_start: 0.6941 (tmm) cc_final: 0.6526 (ttt) REVERT: J 96 THR cc_start: 0.8508 (m) cc_final: 0.8074 (t) REVERT: J 110 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8110 (mtpt) REVERT: J 161 MET cc_start: 0.5106 (mmt) cc_final: 0.4870 (mmm) REVERT: J 184 TYR cc_start: 0.4858 (m-80) cc_final: 0.4546 (m-80) REVERT: J 185 CYS cc_start: 0.5249 (m) cc_final: 0.4829 (m) REVERT: J 188 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6411 (mm-30) REVERT: J 240 MET cc_start: 0.8509 (tmt) cc_final: 0.8278 (tmt) REVERT: J 292 TYR cc_start: 0.8889 (m-80) cc_final: 0.8598 (m-80) REVERT: J 469 TYR cc_start: 0.6880 (t80) cc_final: 0.6326 (t80) REVERT: J 569 MET cc_start: 0.7303 (mpp) cc_final: 0.6341 (mpp) REVERT: J 734 SER cc_start: 0.7885 (m) cc_final: 0.7355 (t) REVERT: J 987 GLN cc_start: 0.3039 (OUTLIER) cc_final: 0.2767 (pm20) REVERT: J 1090 GLU cc_start: 0.8968 (tp30) cc_final: 0.8746 (tp30) REVERT: J 1146 HIS cc_start: 0.5059 (OUTLIER) cc_final: 0.2774 (m-70) REVERT: J 1210 THR cc_start: 0.0703 (OUTLIER) cc_final: 0.0338 (p) REVERT: K 27 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: K 80 GLU cc_start: 0.7271 (mp0) cc_final: 0.6896 (pm20) REVERT: K 155 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5140 (mt) outliers start: 159 outliers final: 68 residues processed: 449 average time/residue: 0.5750 time to fit residues: 324.6071 Evaluate side-chains 348 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 270 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 421 ASN Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 757 MET Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 771 ASP Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1055 ILE Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1175 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 1180 ILE Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 741 THR Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 941 VAL Chi-restraints excluded: chain J residue 987 GLN Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1151 SER Chi-restraints excluded: chain J residue 1180 ILE Chi-restraints excluded: chain J residue 1210 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 50 TYR Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 96 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 380 optimal weight: 3.9990 chunk 430 optimal weight: 3.9990 chunk 39 optimal weight: 40.0000 chunk 464 optimal weight: 4.9990 chunk 377 optimal weight: 6.9990 chunk 70 optimal weight: 30.0000 chunk 114 optimal weight: 2.9990 chunk 448 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS G 348 HIS G1009 GLN G1023 GLN ** G1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1169 ASN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 ASN I 769 GLN I1056 GLN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS J 236 ASN J 261 GLN ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 769 GLN J1146 HIS J1208 GLN J1212 GLN K 6 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.169309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.138101 restraints weight = 170209.694| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 5.00 r_work: 0.3912 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 1.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 38026 Z= 0.361 Angle : 0.982 16.166 51790 Z= 0.519 Chirality : 0.056 0.494 5813 Planarity : 0.007 0.090 6698 Dihedral : 6.799 59.625 5269 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.82 % Favored : 89.87 % Rotamer: Outliers : 5.10 % Allowed : 26.32 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.11), residues: 4813 helix: -0.14 (0.19), residues: 750 sheet: -0.79 (0.15), residues: 1257 loop : -2.31 (0.10), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 38 TYR 0.067 0.003 TYR G 314 PHE 0.072 0.004 PHE J1136 TRP 0.051 0.003 TRP G 44 HIS 0.025 0.002 HIS J1146 Details of bonding type rmsd covalent geometry : bond 0.00805 (37966) covalent geometry : angle 0.97894 (51670) SS BOND : bond 0.00778 ( 60) SS BOND : angle 1.96888 ( 120) hydrogen bonds : bond 0.06626 ( 1237) hydrogen bonds : angle 7.06718 ( 3211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 332 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.5827 (ttp80) cc_final: 0.5524 (pmt-80) REVERT: E 148 LEU cc_start: 0.1703 (mt) cc_final: 0.1298 (pp) REVERT: F 6 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6881 (mt0) REVERT: F 37 TYR cc_start: 0.6034 (m-80) cc_final: 0.5475 (m-80) REVERT: G 31 ILE cc_start: 0.0445 (OUTLIER) cc_final: -0.0248 (pt) REVERT: G 84 MET cc_start: 0.7149 (tmm) cc_final: 0.6665 (tpt) REVERT: G 143 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (tt) REVERT: G 148 MET cc_start: 0.6756 (tmt) cc_final: 0.5658 (mtt) REVERT: G 433 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8746 (pt) REVERT: G 438 TYR cc_start: 0.7658 (m-10) cc_final: 0.7432 (m-10) REVERT: G 448 TYR cc_start: 0.7687 (t80) cc_final: 0.7464 (t80) REVERT: G 481 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9024 (pp) REVERT: G 497 TYR cc_start: 0.6946 (m-80) cc_final: 0.6627 (m-80) REVERT: G 563 MET cc_start: 0.6769 (tpt) cc_final: 0.5597 (tpt) REVERT: G 569 MET cc_start: 0.8514 (tmt) cc_final: 0.8049 (tmt) REVERT: G 571 PHE cc_start: 0.9452 (m-80) cc_final: 0.8742 (m-80) REVERT: G 628 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6837 (mt0) REVERT: G 699 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6990 (mmp80) REVERT: G 772 GLN cc_start: 0.4033 (OUTLIER) cc_final: 0.3069 (tt0) REVERT: G 869 PHE cc_start: 0.0753 (OUTLIER) cc_final: 0.0339 (m-80) REVERT: G 1141 TYR cc_start: 0.1540 (OUTLIER) cc_final: 0.1179 (t80) REVERT: H 29 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7505 (t80) REVERT: H 80 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: I 184 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: I 985 ILE cc_start: 0.1492 (OUTLIER) cc_final: 0.0609 (tp) REVERT: I 1189 SER cc_start: -0.0691 (OUTLIER) cc_final: -0.2056 (p) REVERT: J 18 TYR cc_start: 0.7928 (m-80) cc_final: 0.7387 (m-80) REVERT: J 96 THR cc_start: 0.8646 (m) cc_final: 0.8272 (t) REVERT: J 110 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: J 185 CYS cc_start: 0.5377 (m) cc_final: 0.5172 (m) REVERT: J 188 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6795 (mm-30) REVERT: J 240 MET cc_start: 0.8508 (tmt) cc_final: 0.8201 (tmt) REVERT: J 428 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7730 (tt) REVERT: J 569 MET cc_start: 0.7150 (mpp) cc_final: 0.6125 (mpp) REVERT: J 840 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9318 (mp) REVERT: J 859 SER cc_start: 0.2870 (OUTLIER) cc_final: 0.2393 (m) REVERT: J 1090 GLU cc_start: 0.8901 (tp30) cc_final: 0.8695 (tp30) REVERT: J 1126 PHE cc_start: 0.7685 (m-10) cc_final: 0.7133 (m-80) REVERT: J 1127 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9077 (p) REVERT: J 1151 SER cc_start: 0.6992 (m) cc_final: 0.6535 (p) REVERT: K 24 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7905 (tpt-90) REVERT: K 27 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: K 155 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5992 (mt) outliers start: 211 outliers final: 92 residues processed: 504 average time/residue: 0.5099 time to fit residues: 327.4866 Evaluate side-chains 395 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 281 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 314 TYR Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 423 PHE Chi-restraints excluded: chain G residue 433 ILE Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 629 ARG Chi-restraints excluded: chain G residue 699 ARG Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 718 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 772 GLN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 869 PHE Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1138 HIS Chi-restraints excluded: chain G residue 1141 TYR Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1218 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 533 THR Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 724 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 873 LEU Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1189 SER Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 584 VAL Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 621 THR Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 717 LEU Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 840 LEU Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1205 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 377 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 480 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 416 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 470 optimal weight: 6.9990 chunk 408 optimal weight: 3.9990 chunk 399 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN G1169 ASN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN I 208 HIS I 298 HIS I 408 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1160 ASN J1217 ASN K 148 GLN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.139654 restraints weight = 185337.157| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 5.26 r_work: 0.3940 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3938 r_free = 0.3938 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 1.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38026 Z= 0.165 Angle : 0.757 15.147 51790 Z= 0.389 Chirality : 0.047 0.335 5813 Planarity : 0.005 0.076 6698 Dihedral : 5.967 51.885 5264 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.05 % Favored : 91.68 % Rotamer: Outliers : 3.89 % Allowed : 27.70 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4813 helix: 0.30 (0.19), residues: 757 sheet: -0.81 (0.14), residues: 1272 loop : -2.10 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.036 0.002 TYR F 88 PHE 0.031 0.002 PHE J 788 TRP 0.057 0.002 TRP E 47 HIS 0.012 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00372 (37966) covalent geometry : angle 0.75348 (51670) SS BOND : bond 0.00383 ( 60) SS BOND : angle 1.66351 ( 120) hydrogen bonds : bond 0.04823 ( 1237) hydrogen bonds : angle 6.26255 ( 3211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 295 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.5897 (ttp80) cc_final: 0.5540 (pmt-80) REVERT: C 38 GLN cc_start: 0.4110 (tp40) cc_final: 0.2935 (mm-40) REVERT: C 72 PHE cc_start: 0.6248 (m-80) cc_final: 0.5083 (t80) REVERT: C 91 GLN cc_start: 0.5305 (tm130) cc_final: 0.4412 (tt0) REVERT: E 48 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7161 (mmt) REVERT: F 37 TYR cc_start: 0.6119 (m-80) cc_final: 0.5690 (m-80) REVERT: G 31 ILE cc_start: 0.1198 (OUTLIER) cc_final: 0.0571 (pt) REVERT: G 84 MET cc_start: 0.7294 (tmm) cc_final: 0.6789 (tpt) REVERT: G 143 ILE cc_start: 0.7600 (tp) cc_final: 0.7260 (tt) REVERT: G 148 MET cc_start: 0.6931 (tmt) cc_final: 0.5759 (mtm) REVERT: G 221 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6241 (mtp180) REVERT: G 448 TYR cc_start: 0.7692 (t80) cc_final: 0.6901 (t80) REVERT: G 480 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8728 (tp) REVERT: G 481 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9231 (mm) REVERT: G 497 TYR cc_start: 0.6931 (m-80) cc_final: 0.6370 (m-80) REVERT: G 535 TRP cc_start: 0.8696 (t-100) cc_final: 0.8285 (t60) REVERT: G 563 MET cc_start: 0.6739 (tpt) cc_final: 0.5536 (tpt) REVERT: G 571 PHE cc_start: 0.9411 (m-80) cc_final: 0.8856 (m-80) REVERT: G 700 ARG cc_start: 0.6160 (ptt180) cc_final: 0.5678 (ptt-90) REVERT: G 772 GLN cc_start: 0.2863 (OUTLIER) cc_final: 0.2192 (tt0) REVERT: G 950 SER cc_start: 0.6937 (m) cc_final: 0.6529 (p) REVERT: G 985 ILE cc_start: -0.4016 (OUTLIER) cc_final: -0.4755 (mp) REVERT: G 1101 ASP cc_start: 0.8269 (m-30) cc_final: 0.7995 (m-30) REVERT: I 133 SER cc_start: 0.8605 (t) cc_final: 0.8301 (t) REVERT: I 259 THR cc_start: 0.8256 (p) cc_final: 0.7945 (p) REVERT: I 306 ASP cc_start: 0.7816 (t0) cc_final: 0.6746 (p0) REVERT: I 717 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9037 (mp) REVERT: I 871 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (pp) REVERT: I 985 ILE cc_start: 0.1635 (OUTLIER) cc_final: 0.0480 (tp) REVERT: I 1090 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: I 1189 SER cc_start: -0.1474 (OUTLIER) cc_final: -0.2372 (p) REVERT: J 96 THR cc_start: 0.8736 (m) cc_final: 0.8403 (t) REVERT: J 110 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (mtpt) REVERT: J 167 HIS cc_start: 0.6932 (OUTLIER) cc_final: 0.6643 (t-170) REVERT: J 171 LEU cc_start: 0.8156 (tt) cc_final: 0.7899 (mt) REVERT: J 240 MET cc_start: 0.8470 (tmt) cc_final: 0.8085 (tmt) REVERT: J 292 TYR cc_start: 0.8983 (m-80) cc_final: 0.8747 (m-80) REVERT: J 295 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8696 (mp) REVERT: J 428 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7691 (tt) REVERT: J 569 MET cc_start: 0.7190 (mpp) cc_final: 0.6206 (mpp) REVERT: J 765 ASN cc_start: 0.8053 (t0) cc_final: 0.7248 (t0) REVERT: J 859 SER cc_start: 0.2972 (OUTLIER) cc_final: 0.2727 (p) REVERT: K 27 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: K 50 TYR cc_start: 0.7433 (p90) cc_final: 0.7145 (p90) outliers start: 161 outliers final: 77 residues processed: 428 average time/residue: 0.5475 time to fit residues: 296.0189 Evaluate side-chains 361 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 266 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 63 PHE Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 156 PHE Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 421 ASN Chi-restraints excluded: chain G residue 423 PHE Chi-restraints excluded: chain G residue 480 ILE Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 714 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 772 GLN Chi-restraints excluded: chain G residue 985 ILE Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1138 HIS Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 533 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 766 HIS Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 871 LEU Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1189 SER Chi-restraints excluded: chain I residue 1222 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 412 THR Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 734 SER Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 856 SER Chi-restraints excluded: chain J residue 859 SER Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1124 VAL Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1205 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Chi-restraints excluded: chain K residue 211 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 352 optimal weight: 5.9990 chunk 281 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 288 optimal weight: 3.9990 chunk 434 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 377 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS C 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 65 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN G1110 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1169 ASN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 HIS I 408 ASN I 599 GLN I 766 HIS ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1212 GLN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 566 GLN ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 765 ASN J 800 GLN ** J1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** 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 = 0.4593 r_free = 0.4593 target = 0.164525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.129595 restraints weight = 151411.252| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 5.50 r_work: 0.3812 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 1.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 38026 Z= 0.307 Angle : 0.886 12.513 51790 Z= 0.463 Chirality : 0.053 0.363 5813 Planarity : 0.006 0.120 6698 Dihedral : 6.545 57.525 5264 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.48 % Favored : 90.25 % Rotamer: Outliers : 4.18 % Allowed : 27.50 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.11), residues: 4813 helix: -0.12 (0.19), residues: 749 sheet: -0.90 (0.14), residues: 1310 loop : -2.11 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 38 TYR 0.040 0.003 TYR G1142 PHE 0.094 0.003 PHE G 423 TRP 0.056 0.003 TRP E 47 HIS 0.016 0.002 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00714 (37966) covalent geometry : angle 0.88292 (51670) SS BOND : bond 0.00611 ( 60) SS BOND : angle 1.69654 ( 120) hydrogen bonds : bond 0.06064 ( 1237) hydrogen bonds : angle 6.74501 ( 3211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 313 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLN cc_start: 0.4146 (tp40) cc_final: 0.3397 (mm-40) REVERT: E 48 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7356 (mmt) REVERT: F 37 TYR cc_start: 0.6107 (m-80) cc_final: 0.5592 (m-80) REVERT: G 31 ILE cc_start: 0.1808 (OUTLIER) cc_final: 0.1297 (pt) REVERT: G 142 LYS cc_start: 0.4706 (OUTLIER) cc_final: 0.4393 (ptpt) REVERT: G 143 ILE cc_start: 0.8075 (tp) cc_final: 0.7633 (mt) REVERT: G 144 TYR cc_start: 0.6211 (m-80) cc_final: 0.5595 (m-80) REVERT: G 163 ARG cc_start: 0.4139 (ttm110) cc_final: 0.3271 (ttt180) REVERT: G 221 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7031 (mtp180) REVERT: G 245 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6651 (mt) REVERT: G 252 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: G 270 TYR cc_start: 0.4948 (m-80) cc_final: 0.3873 (m-80) REVERT: G 281 PHE cc_start: 0.7009 (t80) cc_final: 0.6643 (p90) REVERT: G 448 TYR cc_start: 0.7942 (t80) cc_final: 0.7213 (t80) REVERT: G 497 TYR cc_start: 0.7128 (m-80) cc_final: 0.6634 (m-80) REVERT: G 535 TRP cc_start: 0.8747 (t-100) cc_final: 0.8382 (t60) REVERT: G 563 MET cc_start: 0.6990 (tpt) cc_final: 0.5905 (tpt) REVERT: G 628 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: G 700 ARG cc_start: 0.7184 (ptt180) cc_final: 0.6698 (ppt-90) REVERT: G 772 GLN cc_start: 0.3753 (OUTLIER) cc_final: 0.3156 (tt0) REVERT: G 857 GLN cc_start: 0.5013 (mt0) cc_final: 0.4679 (tt0) REVERT: G 906 MET cc_start: 0.8149 (ttt) cc_final: 0.7917 (ttt) REVERT: G 1191 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3691 (m-80) REVERT: H 191 VAL cc_start: 0.7443 (m) cc_final: 0.7123 (t) REVERT: I 165 PHE cc_start: 0.6593 (t80) cc_final: 0.6246 (t80) REVERT: I 184 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: I 259 THR cc_start: 0.8290 (p) cc_final: 0.7973 (p) REVERT: I 717 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.9197 (mp) REVERT: I 985 ILE cc_start: 0.2490 (OUTLIER) cc_final: 0.1846 (mm) REVERT: I 1189 SER cc_start: -0.0830 (OUTLIER) cc_final: -0.2039 (p) REVERT: J 110 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8016 (mtpt) REVERT: J 240 MET cc_start: 0.8492 (tmt) cc_final: 0.8091 (tmt) REVERT: J 292 TYR cc_start: 0.9000 (m-80) cc_final: 0.8755 (m-80) REVERT: J 441 LEU cc_start: 0.9172 (tt) cc_final: 0.8927 (mm) REVERT: J 571 PHE cc_start: 0.8537 (m-80) cc_final: 0.8325 (m-80) REVERT: J 666 GLU cc_start: 0.8207 (pm20) cc_final: 0.7943 (pm20) REVERT: J 907 GLN cc_start: 0.7612 (pm20) cc_final: 0.7313 (pp30) REVERT: J 954 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7966 (p) REVERT: K 27 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: K 50 TYR cc_start: 0.7651 (p90) cc_final: 0.7379 (p90) REVERT: K 170 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7489 (mmmt) outliers start: 173 outliers final: 94 residues processed: 457 average time/residue: 0.3578 time to fit residues: 206.7013 Evaluate side-chains 392 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 281 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 343 ASP Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 588 LEU Chi-restraints excluded: chain G residue 628 GLN Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 772 GLN Chi-restraints excluded: chain G residue 853 VAL Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 948 THR Chi-restraints excluded: chain G residue 1031 GLN Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1191 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 424 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 533 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 845 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1031 GLN Chi-restraints excluded: chain I residue 1090 GLU Chi-restraints excluded: chain I residue 1189 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 362 SER Chi-restraints excluded: chain J residue 389 LEU Chi-restraints excluded: chain J residue 412 THR Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 620 CYS Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain J residue 808 GLN Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 954 SER Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1205 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 261 optimal weight: 0.0980 chunk 452 optimal weight: 4.9990 chunk 389 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 405 optimal weight: 0.7980 chunk 477 optimal weight: 8.9990 chunk 411 optimal weight: 3.9990 chunk 313 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 GLN G 999 ASN G1023 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1169 ASN ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 GLN I 599 GLN I 974 GLN ** I 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1020 GLN ** I1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 774 ASN J1009 GLN J1145 ASN K 148 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.165972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.132502 restraints weight = 151660.155| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 4.68 r_work: 0.3869 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 1.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 38026 Z= 0.162 Angle : 0.763 15.791 51790 Z= 0.389 Chirality : 0.047 0.319 5813 Planarity : 0.005 0.074 6698 Dihedral : 5.957 52.205 5264 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.32 % Favored : 91.41 % Rotamer: Outliers : 3.10 % Allowed : 28.79 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.12), residues: 4813 helix: 0.36 (0.20), residues: 741 sheet: -0.80 (0.14), residues: 1259 loop : -2.01 (0.11), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 24 TYR 0.044 0.002 TYR F 33 PHE 0.068 0.002 PHE G 399 TRP 0.058 0.002 TRP E 47 HIS 0.011 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00370 (37966) covalent geometry : angle 0.76063 (51670) SS BOND : bond 0.00335 ( 60) SS BOND : angle 1.37890 ( 120) hydrogen bonds : bond 0.04726 ( 1237) hydrogen bonds : angle 6.14413 ( 3211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 301 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 GLN cc_start: 0.4146 (tp40) cc_final: 0.3114 (mm-40) REVERT: C 91 GLN cc_start: 0.5688 (tm130) cc_final: 0.4727 (tt0) REVERT: E 48 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7106 (mmt) REVERT: F 37 TYR cc_start: 0.6102 (m-80) cc_final: 0.5639 (m-80) REVERT: G 31 ILE cc_start: 0.1627 (OUTLIER) cc_final: 0.1154 (pt) REVERT: G 142 LYS cc_start: 0.5516 (OUTLIER) cc_final: 0.5216 (ptpt) REVERT: G 144 TYR cc_start: 0.5494 (m-80) cc_final: 0.4887 (m-80) REVERT: G 163 ARG cc_start: 0.4038 (ttm110) cc_final: 0.3477 (mtm110) REVERT: G 221 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6790 (mtp180) REVERT: G 270 TYR cc_start: 0.4962 (m-80) cc_final: 0.4411 (m-80) REVERT: G 497 TYR cc_start: 0.7058 (m-80) cc_final: 0.6551 (m-80) REVERT: G 535 TRP cc_start: 0.8823 (t-100) cc_final: 0.8490 (t60) REVERT: G 563 MET cc_start: 0.6920 (tpt) cc_final: 0.5826 (tpt) REVERT: G 757 MET cc_start: 0.9204 (mtt) cc_final: 0.8923 (mtt) REVERT: G 772 GLN cc_start: 0.2891 (OUTLIER) cc_final: 0.2539 (mm-40) REVERT: G 906 MET cc_start: 0.8020 (ttt) cc_final: 0.7743 (ttt) REVERT: G 1105 GLU cc_start: 0.8573 (tp30) cc_final: 0.8171 (tm-30) REVERT: G 1137 MET cc_start: 0.6187 (pmt) cc_final: 0.5889 (ttm) REVERT: G 1191 PHE cc_start: 0.3592 (OUTLIER) cc_final: 0.3257 (m-80) REVERT: H 191 VAL cc_start: 0.7593 (m) cc_final: 0.7203 (t) REVERT: I 163 ARG cc_start: 0.7241 (tpt-90) cc_final: 0.6684 (tmm160) REVERT: I 169 LEU cc_start: 0.8484 (tt) cc_final: 0.8267 (tm) REVERT: I 184 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: I 259 THR cc_start: 0.8263 (p) cc_final: 0.7960 (p) REVERT: I 717 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9065 (mp) REVERT: I 985 ILE cc_start: 0.1275 (OUTLIER) cc_final: 0.0514 (mm) REVERT: I 993 ASN cc_start: 0.6995 (m-40) cc_final: 0.6744 (m110) REVERT: I 1189 SER cc_start: -0.1889 (OUTLIER) cc_final: -0.2603 (p) REVERT: J 110 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7972 (mtpt) REVERT: J 240 MET cc_start: 0.8480 (tmt) cc_final: 0.8089 (tmt) REVERT: J 289 THR cc_start: 0.9088 (m) cc_final: 0.8842 (t) REVERT: J 292 TYR cc_start: 0.8982 (m-80) cc_final: 0.8719 (m-80) REVERT: J 428 ILE cc_start: 0.7959 (mp) cc_final: 0.7476 (tt) REVERT: J 569 MET cc_start: 0.7549 (mpp) cc_final: 0.5935 (mpp) REVERT: J 774 ASN cc_start: 0.3258 (OUTLIER) cc_final: 0.2880 (t160) REVERT: J 907 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6936 (pp30) REVERT: K 27 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: K 50 TYR cc_start: 0.7521 (p90) cc_final: 0.7254 (p90) REVERT: K 146 LYS cc_start: 0.7766 (tmmm) cc_final: 0.6680 (mmtp) outliers start: 128 outliers final: 80 residues processed: 407 average time/residue: 0.3610 time to fit residues: 185.8734 Evaluate side-chains 369 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 275 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 772 GLN Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 1054 ILE Chi-restraints excluded: chain G residue 1059 ASP Chi-restraints excluded: chain G residue 1141 TYR Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1191 PHE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 533 THR Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 717 LEU Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 845 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1189 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 412 THR Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 573 ILE Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 620 CYS Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 774 ASN Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 907 GLN Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1146 HIS Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 51 optimal weight: 7.9990 chunk 427 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 395 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 378 optimal weight: 0.0040 chunk 299 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1201 ASN I 107 GLN I 599 GLN ** I 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1145 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 774 ASN J 808 GLN ** J 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN ** J1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.165892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.131586 restraints weight = 174209.994| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 5.06 r_work: 0.3862 rms_B_bonded: 5.02 restraints_weight: 2.0000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 1.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 38026 Z= 0.153 Angle : 0.748 12.800 51790 Z= 0.381 Chirality : 0.047 0.306 5813 Planarity : 0.005 0.085 6698 Dihedral : 5.758 53.166 5264 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.11 % Favored : 91.66 % Rotamer: Outliers : 2.64 % Allowed : 29.41 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.12), residues: 4813 helix: 0.45 (0.20), residues: 752 sheet: -0.82 (0.14), residues: 1303 loop : -1.92 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 50 TYR 0.021 0.002 TYR I 448 PHE 0.043 0.002 PHE G 571 TRP 0.060 0.002 TRP E 47 HIS 0.016 0.001 HIS J 167 Details of bonding type rmsd covalent geometry : bond 0.00353 (37966) covalent geometry : angle 0.74590 (51670) SS BOND : bond 0.00366 ( 60) SS BOND : angle 1.31163 ( 120) hydrogen bonds : bond 0.04505 ( 1237) hydrogen bonds : angle 5.95706 ( 3211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9626 Ramachandran restraints generated. 4813 Oldfield, 0 Emsley, 4813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 289 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.5713 (ttp80) cc_final: 0.5305 (pmt-80) REVERT: C 38 GLN cc_start: 0.4172 (tp40) cc_final: 0.2835 (mm-40) REVERT: C 72 PHE cc_start: 0.6028 (m-80) cc_final: 0.5190 (t80) REVERT: C 91 GLN cc_start: 0.5650 (tm130) cc_final: 0.4736 (tt0) REVERT: E 48 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: F 37 TYR cc_start: 0.5904 (m-80) cc_final: 0.5537 (m-80) REVERT: G 31 ILE cc_start: 0.1821 (OUTLIER) cc_final: 0.1405 (pt) REVERT: G 142 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5044 (ptpt) REVERT: G 163 ARG cc_start: 0.4253 (ttm110) cc_final: 0.3723 (mtm180) REVERT: G 221 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6741 (mtp180) REVERT: G 497 TYR cc_start: 0.7052 (m-80) cc_final: 0.6484 (m-80) REVERT: G 535 TRP cc_start: 0.8846 (t-100) cc_final: 0.8528 (t60) REVERT: G 563 MET cc_start: 0.6933 (tpt) cc_final: 0.5517 (tpt) REVERT: G 571 PHE cc_start: 0.9397 (m-80) cc_final: 0.9139 (m-80) REVERT: G 757 MET cc_start: 0.9311 (mtt) cc_final: 0.9029 (mtt) REVERT: G 906 MET cc_start: 0.7984 (ttt) cc_final: 0.7724 (ttt) REVERT: G 1137 MET cc_start: 0.6898 (pmt) cc_final: 0.6466 (ttm) REVERT: G 1191 PHE cc_start: 0.4103 (OUTLIER) cc_final: 0.3541 (m-80) REVERT: H 191 VAL cc_start: 0.7469 (m) cc_final: 0.7172 (t) REVERT: I 163 ARG cc_start: 0.7237 (tpt-90) cc_final: 0.6776 (tmm160) REVERT: I 184 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: I 259 THR cc_start: 0.8242 (p) cc_final: 0.7936 (p) REVERT: I 907 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7592 (tp-100) REVERT: I 985 ILE cc_start: 0.1512 (OUTLIER) cc_final: 0.0611 (mm) REVERT: I 1189 SER cc_start: -0.1327 (OUTLIER) cc_final: -0.2001 (p) REVERT: J 110 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8084 (mtpt) REVERT: J 167 HIS cc_start: 0.7000 (OUTLIER) cc_final: 0.6619 (t-170) REVERT: J 240 MET cc_start: 0.8546 (tmt) cc_final: 0.8177 (tmt) REVERT: J 289 THR cc_start: 0.9100 (m) cc_final: 0.8859 (t) REVERT: J 292 TYR cc_start: 0.8979 (m-80) cc_final: 0.8705 (m-80) REVERT: J 428 ILE cc_start: 0.7990 (mp) cc_final: 0.7475 (tt) REVERT: J 438 TYR cc_start: 0.7549 (m-10) cc_final: 0.7298 (m-10) REVERT: J 569 MET cc_start: 0.7373 (mpp) cc_final: 0.5804 (mpp) REVERT: J 734 SER cc_start: 0.7595 (m) cc_final: 0.7187 (t) REVERT: J 862 ILE cc_start: 0.4167 (OUTLIER) cc_final: 0.3214 (mp) REVERT: J 907 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7263 (pp30) REVERT: K 27 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: K 50 TYR cc_start: 0.7506 (p90) cc_final: 0.7240 (p90) REVERT: K 146 LYS cc_start: 0.7912 (tmmm) cc_final: 0.6879 (mmtm) outliers start: 109 outliers final: 81 residues processed: 382 average time/residue: 0.3590 time to fit residues: 173.9456 Evaluate side-chains 371 residues out of total 4147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 277 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 166 ASN Chi-restraints excluded: chain G residue 221 ARG Chi-restraints excluded: chain G residue 399 PHE Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 446 PHE Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 530 VAL Chi-restraints excluded: chain G residue 734 SER Chi-restraints excluded: chain G residue 761 SER Chi-restraints excluded: chain G residue 858 SER Chi-restraints excluded: chain G residue 1150 VAL Chi-restraints excluded: chain G residue 1191 PHE Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 107 GLN Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain I residue 352 GLU Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 428 ILE Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 526 CYS Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 533 THR Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 621 THR Chi-restraints excluded: chain I residue 623 VAL Chi-restraints excluded: chain I residue 659 VAL Chi-restraints excluded: chain I residue 682 ILE Chi-restraints excluded: chain I residue 718 VAL Chi-restraints excluded: chain I residue 781 SER Chi-restraints excluded: chain I residue 845 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 948 THR Chi-restraints excluded: chain I residue 985 ILE Chi-restraints excluded: chain I residue 1189 SER Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 110 LYS Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 167 HIS Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 412 THR Chi-restraints excluded: chain J residue 526 CYS Chi-restraints excluded: chain J residue 590 PHE Chi-restraints excluded: chain J residue 620 CYS Chi-restraints excluded: chain J residue 623 VAL Chi-restraints excluded: chain J residue 694 ARG Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 907 GLN Chi-restraints excluded: chain J residue 1091 SER Chi-restraints excluded: chain J residue 1149 VAL Chi-restraints excluded: chain J residue 1205 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 157 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 346 optimal weight: 2.9990 chunk 204 optimal weight: 0.1980 chunk 70 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 456 optimal weight: 0.7980 chunk 279 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 412 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1023 GLN ** G1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 GLN I 599 GLN ** I 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1146 HIS J 167 HIS ** J 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 636 GLN J 774 ASN ** J1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.166220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.132071 restraints weight = 170704.414| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 4.85 r_work: 0.3870 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 1.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 38026 Z= 0.143 Angle : 0.744 12.947 51790 Z= 0.377 Chirality : 0.046 0.295 5813 Planarity : 0.005 0.080 6698 Dihedral : 5.600 53.730 5262 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.92 % Favored : 91.87 % Rotamer: Outliers : 2.35 % Allowed : 29.83 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.12), residues: 4813 helix: 0.57 (0.20), residues: 751 sheet: -0.80 (0.14), residues: 1298 loop : -1.89 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 50 TYR 0.049 0.001 TYR F 33 PHE 0.044 0.002 PHE G 571 TRP 0.060 0.002 TRP E 47 HIS 0.007 0.001 HIS G1122 Details of bonding type rmsd covalent geometry : bond 0.00329 (37966) covalent geometry : angle 0.74220 (51670) SS BOND : bond 0.00337 ( 60) SS BOND : angle 1.23901 ( 120) hydrogen bonds : bond 0.04371 ( 1237) hydrogen bonds : angle 5.84301 ( 3211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19443.27 seconds wall clock time: 329 minutes 41.90 seconds (19781.90 seconds total)