Starting phenix.real_space_refine on Mon Mar 18 18:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qok_14093/03_2024/7qok_14093.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 198 5.16 5 C 56364 2.51 5 N 14784 2.21 5 O 17490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 88842 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "D" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "H" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "L" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "N" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "O" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "P" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "T" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 10980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 10980 Classifications: {'peptide': 1361} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1309} Chain breaks: 1 Chain: "V" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "W" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "X" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 226} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 35.00, per 1000 atoms: 0.39 Number of scatterers: 88842 At special positions: 0 Unit cell: (154.745, 154.745, 259.302, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 198 16.00 Mg 6 11.99 O 17490 8.00 N 14784 7.00 C 56364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 24.76 Conformation dependent library (CDL) restraints added in 12.1 seconds 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20952 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 192 sheets defined 18.8% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.81 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE A 22 " --> pdb=" O VAL A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 160 " --> pdb=" O ASP A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.559A pdb=" N LEU A 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 287 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 288 " --> pdb=" O THR A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 288' Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE A 366 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 367 " --> pdb=" O SER A 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 363 through 367' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 490 through 496 removed outlier: 4.227A pdb=" N THR A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR A 526 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN A 580 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.851A pdb=" N TYR A 634 " --> pdb=" O THR A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 774 removed outlier: 3.679A pdb=" N ASN A 774 " --> pdb=" O ILE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU A 793 " --> pdb=" O LYS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU A 811 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 818 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.518A pdb=" N ILE A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR A1006 " --> pdb=" O ASN A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1128 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1161 through 1168 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 26 through 47 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 60 through 69 removed outlier: 4.770A pdb=" N GLU C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 225 Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 14 through 19 removed outlier: 4.764A pdb=" N MET D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 47 Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR D 126 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 207 through 225 Processing helix chain 'D' and resid 226 through 234 Processing helix chain 'D' and resid 235 through 238 removed outlier: 3.970A pdb=" N GLU D 238 " --> pdb=" O GLN D 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 235 through 238' Processing helix chain 'E' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE E 22 " --> pdb=" O VAL E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP E 158 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE E 159 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP E 160 " --> pdb=" O ASP E 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 160' Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.558A pdb=" N LEU E 286 " --> pdb=" O ASP E 283 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 287 " --> pdb=" O PRO E 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 288 " --> pdb=" O THR E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 288' Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE E 366 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 367 " --> pdb=" O SER E 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 363 through 367' Processing helix chain 'E' and resid 425 through 435 Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 490 through 496 removed outlier: 4.228A pdb=" N THR E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR E 526 " --> pdb=" O SER E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 552 Processing helix chain 'E' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU E 573 " --> pdb=" O SER E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN E 580 " --> pdb=" O ARG E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 635 removed outlier: 3.852A pdb=" N TYR E 634 " --> pdb=" O THR E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 769 through 774 removed outlier: 3.679A pdb=" N ASN E 774 " --> pdb=" O ILE E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU E 793 " --> pdb=" O LYS E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU E 811 " --> pdb=" O GLN E 808 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 818 Processing helix chain 'E' and resid 912 through 918 removed outlier: 3.518A pdb=" N ILE E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 981 Processing helix chain 'E' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR E1006 " --> pdb=" O ASN E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1124 through 1128 Processing helix chain 'E' and resid 1155 through 1159 Processing helix chain 'E' and resid 1161 through 1168 Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 26 through 47 Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN G 51 " --> pdb=" O PRO G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'G' and resid 60 through 69 removed outlier: 4.770A pdb=" N GLU G 69 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 225 Processing helix chain 'G' and resid 226 through 235 Processing helix chain 'H' and resid 2 through 14 Processing helix chain 'H' and resid 14 through 19 removed outlier: 4.764A pdb=" N MET H 18 " --> pdb=" O TYR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 47 Processing helix chain 'H' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN H 51 " --> pdb=" O PRO H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 51' Processing helix chain 'H' and resid 60 through 68 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR H 126 " --> pdb=" O TYR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 207 through 225 Processing helix chain 'H' and resid 226 through 234 Processing helix chain 'H' and resid 235 through 238 removed outlier: 3.969A pdb=" N GLU H 238 " --> pdb=" O GLN H 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 235 through 238' Processing helix chain 'I' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE I 22 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP I 158 " --> pdb=" O ASN I 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE I 159 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP I 160 " --> pdb=" O ASP I 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 155 through 160' Processing helix chain 'I' and resid 283 through 288 removed outlier: 3.558A pdb=" N LEU I 286 " --> pdb=" O ASP I 283 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU I 287 " --> pdb=" O PRO I 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU I 288 " --> pdb=" O THR I 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 283 through 288' Processing helix chain 'I' and resid 320 through 331 Processing helix chain 'I' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE I 366 " --> pdb=" O ASP I 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS I 367 " --> pdb=" O SER I 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 363 through 367' Processing helix chain 'I' and resid 425 through 435 Processing helix chain 'I' and resid 467 through 471 Processing helix chain 'I' and resid 490 through 496 removed outlier: 4.228A pdb=" N THR I 494 " --> pdb=" O GLU I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'I' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR I 526 " --> pdb=" O SER I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 552 Processing helix chain 'I' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU I 573 " --> pdb=" O SER I 569 " (cutoff:3.500A) Processing helix chain 'I' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN I 580 " --> pdb=" O ARG I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 631 through 635 removed outlier: 3.851A pdb=" N TYR I 634 " --> pdb=" O THR I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 769 through 774 removed outlier: 3.678A pdb=" N ASN I 774 " --> pdb=" O ILE I 771 " (cutoff:3.500A) Processing helix chain 'I' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU I 793 " --> pdb=" O LYS I 789 " (cutoff:3.500A) Processing helix chain 'I' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU I 811 " --> pdb=" O GLN I 808 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 818 Processing helix chain 'I' and resid 912 through 918 removed outlier: 3.517A pdb=" N ILE I 916 " --> pdb=" O THR I 912 " (cutoff:3.500A) Processing helix chain 'I' and resid 977 through 981 Processing helix chain 'I' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR I1006 " --> pdb=" O ASN I1003 " (cutoff:3.500A) Processing helix chain 'I' and resid 1124 through 1128 Processing helix chain 'I' and resid 1155 through 1159 Processing helix chain 'I' and resid 1161 through 1168 Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 26 through 47 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN K 51 " --> pdb=" O PRO K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 60 through 69 removed outlier: 4.771A pdb=" N GLU K 69 " --> pdb=" O ILE K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR K 126 " --> pdb=" O TYR K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 225 Processing helix chain 'K' and resid 226 through 235 Processing helix chain 'L' and resid 2 through 14 Processing helix chain 'L' and resid 14 through 19 removed outlier: 4.765A pdb=" N MET L 18 " --> pdb=" O TYR L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 47 Processing helix chain 'L' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN L 51 " --> pdb=" O PRO L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR L 126 " --> pdb=" O TYR L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 206 No H-bonds generated for 'chain 'L' and resid 204 through 206' Processing helix chain 'L' and resid 207 through 225 Processing helix chain 'L' and resid 226 through 234 Processing helix chain 'L' and resid 235 through 238 removed outlier: 3.970A pdb=" N GLU L 238 " --> pdb=" O GLN L 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 235 through 238' Processing helix chain 'M' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE M 22 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP M 158 " --> pdb=" O ASN M 155 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE M 159 " --> pdb=" O ALA M 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP M 160 " --> pdb=" O ASP M 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 155 through 160' Processing helix chain 'M' and resid 283 through 288 removed outlier: 3.559A pdb=" N LEU M 286 " --> pdb=" O ASP M 283 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU M 287 " --> pdb=" O PRO M 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU M 288 " --> pdb=" O THR M 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 283 through 288' Processing helix chain 'M' and resid 320 through 331 Processing helix chain 'M' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE M 366 " --> pdb=" O ASP M 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS M 367 " --> pdb=" O SER M 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 363 through 367' Processing helix chain 'M' and resid 425 through 435 Processing helix chain 'M' and resid 467 through 471 Processing helix chain 'M' and resid 490 through 496 removed outlier: 4.227A pdb=" N THR M 494 " --> pdb=" O GLU M 490 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing helix chain 'M' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR M 526 " --> pdb=" O SER M 523 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 552 Processing helix chain 'M' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU M 573 " --> pdb=" O SER M 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN M 580 " --> pdb=" O ARG M 577 " (cutoff:3.500A) Processing helix chain 'M' and resid 631 through 635 removed outlier: 3.851A pdb=" N TYR M 634 " --> pdb=" O THR M 631 " (cutoff:3.500A) Processing helix chain 'M' and resid 769 through 774 removed outlier: 3.679A pdb=" N ASN M 774 " --> pdb=" O ILE M 771 " (cutoff:3.500A) Processing helix chain 'M' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU M 793 " --> pdb=" O LYS M 789 " (cutoff:3.500A) Processing helix chain 'M' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU M 811 " --> pdb=" O GLN M 808 " (cutoff:3.500A) Processing helix chain 'M' and resid 815 through 818 Processing helix chain 'M' and resid 912 through 918 removed outlier: 3.518A pdb=" N ILE M 916 " --> pdb=" O THR M 912 " (cutoff:3.500A) Processing helix chain 'M' and resid 977 through 981 Processing helix chain 'M' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR M1006 " --> pdb=" O ASN M1003 " (cutoff:3.500A) Processing helix chain 'M' and resid 1124 through 1128 Processing helix chain 'M' and resid 1155 through 1159 Processing helix chain 'M' and resid 1161 through 1168 Processing helix chain 'N' and resid 2 through 8 Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 26 through 47 Processing helix chain 'O' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN O 51 " --> pdb=" O PRO O 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 48 through 51' Processing helix chain 'O' and resid 60 through 69 removed outlier: 4.770A pdb=" N GLU O 69 " --> pdb=" O ILE O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR O 126 " --> pdb=" O TYR O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 225 Processing helix chain 'O' and resid 226 through 235 Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 14 through 19 removed outlier: 4.764A pdb=" N MET P 18 " --> pdb=" O TYR P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 47 Processing helix chain 'P' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN P 51 " --> pdb=" O PRO P 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 48 through 51' Processing helix chain 'P' and resid 60 through 68 Processing helix chain 'P' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR P 126 " --> pdb=" O TYR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 206 No H-bonds generated for 'chain 'P' and resid 204 through 206' Processing helix chain 'P' and resid 207 through 225 Processing helix chain 'P' and resid 226 through 234 Processing helix chain 'P' and resid 235 through 238 removed outlier: 3.970A pdb=" N GLU P 238 " --> pdb=" O GLN P 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 235 through 238' Processing helix chain 'Q' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE Q 22 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP Q 158 " --> pdb=" O ASN Q 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE Q 159 " --> pdb=" O ALA Q 156 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP Q 160 " --> pdb=" O ASP Q 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 155 through 160' Processing helix chain 'Q' and resid 283 through 288 removed outlier: 3.558A pdb=" N LEU Q 286 " --> pdb=" O ASP Q 283 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Q 287 " --> pdb=" O PRO Q 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU Q 288 " --> pdb=" O THR Q 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 283 through 288' Processing helix chain 'Q' and resid 320 through 331 Processing helix chain 'Q' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE Q 366 " --> pdb=" O ASP Q 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 363 through 367' Processing helix chain 'Q' and resid 425 through 435 Processing helix chain 'Q' and resid 467 through 471 Processing helix chain 'Q' and resid 490 through 496 removed outlier: 4.228A pdb=" N THR Q 494 " --> pdb=" O GLU Q 490 " (cutoff:3.500A) Processing helix chain 'Q' and resid 502 through 506 Processing helix chain 'Q' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR Q 526 " --> pdb=" O SER Q 523 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 552 Processing helix chain 'Q' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU Q 573 " --> pdb=" O SER Q 569 " (cutoff:3.500A) Processing helix chain 'Q' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN Q 580 " --> pdb=" O ARG Q 577 " (cutoff:3.500A) Processing helix chain 'Q' and resid 631 through 635 removed outlier: 3.852A pdb=" N TYR Q 634 " --> pdb=" O THR Q 631 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 774 removed outlier: 3.680A pdb=" N ASN Q 774 " --> pdb=" O ILE Q 771 " (cutoff:3.500A) Processing helix chain 'Q' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU Q 793 " --> pdb=" O LYS Q 789 " (cutoff:3.500A) Processing helix chain 'Q' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU Q 811 " --> pdb=" O GLN Q 808 " (cutoff:3.500A) Processing helix chain 'Q' and resid 815 through 818 Processing helix chain 'Q' and resid 912 through 918 removed outlier: 3.519A pdb=" N ILE Q 916 " --> pdb=" O THR Q 912 " (cutoff:3.500A) Processing helix chain 'Q' and resid 977 through 981 Processing helix chain 'Q' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR Q1006 " --> pdb=" O ASN Q1003 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1124 through 1128 Processing helix chain 'Q' and resid 1155 through 1159 Processing helix chain 'Q' and resid 1161 through 1168 Processing helix chain 'R' and resid 2 through 8 Processing helix chain 'S' and resid 2 through 15 Processing helix chain 'S' and resid 26 through 47 Processing helix chain 'S' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN S 51 " --> pdb=" O PRO S 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 48 through 51' Processing helix chain 'S' and resid 60 through 69 removed outlier: 4.770A pdb=" N GLU S 69 " --> pdb=" O ILE S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR S 126 " --> pdb=" O TYR S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 225 Processing helix chain 'S' and resid 226 through 235 Processing helix chain 'T' and resid 2 through 14 Processing helix chain 'T' and resid 14 through 19 removed outlier: 4.764A pdb=" N MET T 18 " --> pdb=" O TYR T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 47 Processing helix chain 'T' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN T 51 " --> pdb=" O PRO T 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 48 through 51' Processing helix chain 'T' and resid 60 through 68 Processing helix chain 'T' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR T 126 " --> pdb=" O TYR T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 206 No H-bonds generated for 'chain 'T' and resid 204 through 206' Processing helix chain 'T' and resid 207 through 225 Processing helix chain 'T' and resid 226 through 234 Processing helix chain 'T' and resid 235 through 238 removed outlier: 3.970A pdb=" N GLU T 238 " --> pdb=" O GLN T 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 235 through 238' Processing helix chain 'U' and resid 18 through 22 removed outlier: 3.543A pdb=" N PHE U 22 " --> pdb=" O VAL U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 155 through 160 removed outlier: 3.700A pdb=" N ASP U 158 " --> pdb=" O ASN U 155 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE U 159 " --> pdb=" O ALA U 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP U 160 " --> pdb=" O ASP U 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 155 through 160' Processing helix chain 'U' and resid 283 through 288 removed outlier: 3.558A pdb=" N LEU U 286 " --> pdb=" O ASP U 283 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU U 287 " --> pdb=" O PRO U 284 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU U 288 " --> pdb=" O THR U 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 283 through 288' Processing helix chain 'U' and resid 320 through 331 Processing helix chain 'U' and resid 363 through 367 removed outlier: 3.653A pdb=" N ILE U 366 " --> pdb=" O ASP U 363 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS U 367 " --> pdb=" O SER U 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 363 through 367' Processing helix chain 'U' and resid 425 through 435 Processing helix chain 'U' and resid 467 through 471 Processing helix chain 'U' and resid 490 through 496 removed outlier: 4.228A pdb=" N THR U 494 " --> pdb=" O GLU U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 502 through 506 Processing helix chain 'U' and resid 521 through 528 removed outlier: 6.107A pdb=" N THR U 526 " --> pdb=" O SER U 523 " (cutoff:3.500A) Processing helix chain 'U' and resid 546 through 552 Processing helix chain 'U' and resid 569 through 575 removed outlier: 3.781A pdb=" N GLU U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 576 through 580 removed outlier: 3.839A pdb=" N ASN U 580 " --> pdb=" O ARG U 577 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 635 removed outlier: 3.851A pdb=" N TYR U 634 " --> pdb=" O THR U 631 " (cutoff:3.500A) Processing helix chain 'U' and resid 769 through 774 removed outlier: 3.679A pdb=" N ASN U 774 " --> pdb=" O ILE U 771 " (cutoff:3.500A) Processing helix chain 'U' and resid 789 through 796 removed outlier: 3.556A pdb=" N LEU U 793 " --> pdb=" O LYS U 789 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 811 removed outlier: 3.970A pdb=" N LEU U 811 " --> pdb=" O GLN U 808 " (cutoff:3.500A) Processing helix chain 'U' and resid 815 through 818 Processing helix chain 'U' and resid 912 through 918 removed outlier: 3.518A pdb=" N ILE U 916 " --> pdb=" O THR U 912 " (cutoff:3.500A) Processing helix chain 'U' and resid 977 through 981 Processing helix chain 'U' and resid 1003 through 1007 removed outlier: 3.666A pdb=" N TYR U1006 " --> pdb=" O ASN U1003 " (cutoff:3.500A) Processing helix chain 'U' and resid 1124 through 1128 Processing helix chain 'U' and resid 1155 through 1159 Processing helix chain 'U' and resid 1161 through 1168 Processing helix chain 'V' and resid 2 through 8 Processing helix chain 'W' and resid 2 through 15 Processing helix chain 'W' and resid 26 through 47 Processing helix chain 'W' and resid 48 through 51 removed outlier: 3.723A pdb=" N ASN W 51 " --> pdb=" O PRO W 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 48 through 51' Processing helix chain 'W' and resid 60 through 69 removed outlier: 4.771A pdb=" N GLU W 69 " --> pdb=" O ILE W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 129 removed outlier: 3.664A pdb=" N THR W 126 " --> pdb=" O TYR W 122 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 225 Processing helix chain 'W' and resid 226 through 235 Processing helix chain 'X' and resid 2 through 14 Processing helix chain 'X' and resid 14 through 19 removed outlier: 4.765A pdb=" N MET X 18 " --> pdb=" O TYR X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 47 Processing helix chain 'X' and resid 48 through 51 removed outlier: 3.699A pdb=" N ASN X 51 " --> pdb=" O PRO X 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 48 through 51' Processing helix chain 'X' and resid 60 through 68 Processing helix chain 'X' and resid 121 through 129 removed outlier: 3.650A pdb=" N THR X 126 " --> pdb=" O TYR X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 206 No H-bonds generated for 'chain 'X' and resid 204 through 206' Processing helix chain 'X' and resid 207 through 225 Processing helix chain 'X' and resid 226 through 234 Processing helix chain 'X' and resid 235 through 238 removed outlier: 3.971A pdb=" N GLU X 238 " --> pdb=" O GLN X 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 235 through 238' Processing sheet with id= 1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE A1370 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE A1272 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A1325 " --> pdb=" O LYS A1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A1322 " --> pdb=" O ILE A1325 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE A1370 " --> pdb=" O PHE A1272 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE A1272 " --> pdb=" O PHE A1370 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE A1256 " --> pdb=" O MET A1352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A1348 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A1346 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A1307 " --> pdb=" O LEU A1296 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id= 5, first strand: chain 'A' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET A1238 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A1222 " --> pdb=" O PHE A1233 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 71 through 73 removed outlier: 7.034A pdb=" N PHE A 84 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 108 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 94 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE A 106 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU A 96 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 121 through 126 Processing sheet with id= 8, first strand: chain 'A' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER A 226 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLY A 180 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N THR A 224 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 229 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG A 205 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 185 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG A 205 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 194 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 242 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 263 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER A 247 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS A 261 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS A 249 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL A 259 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE A 308 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 301 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 299 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 295 through 296 removed outlier: 7.544A pdb=" N SER A1031 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR A 313 " --> pdb=" O PRO A1029 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 332 through 338 removed outlier: 3.510A pdb=" N LYS A 404 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 332 through 338 Processing sheet with id= 15, first strand: chain 'A' and resid 395 through 398 removed outlier: 4.218A pdb=" N GLY A 395 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 376 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 439 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 395 through 398 removed outlier: 4.218A pdb=" N GLY A 395 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 376 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 439 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 582 through 584 removed outlier: 6.492A pdb=" N THR A 582 " --> pdb=" O SER A 731 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER A 731 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 837 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN A 563 " --> pdb=" O CYS A 461 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N CYS A 461 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL A 565 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ILE A 459 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET A 567 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN A 457 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 899 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN A 457 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 897 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 896 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 539 through 540 Processing sheet with id= 19, first strand: chain 'A' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN A 703 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 597 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A 701 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR A 599 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A 699 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A 971 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN A 703 " --> pdb=" O MET A 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU A 973 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A 966 " --> pdb=" O ARG A 952 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 602 through 607 removed outlier: 6.654A pdb=" N ASP A 602 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE A 695 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER A 604 " --> pdb=" O LYS A 693 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS A 693 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 606 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER A 963 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS A 693 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.519A pdb=" N GLY A 642 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 644 " --> pdb=" O TRP A 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP A 664 " --> pdb=" O PHE A 644 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 737 through 739 Processing sheet with id= 23, first strand: chain 'A' and resid 776 through 777 Processing sheet with id= 24, first strand: chain 'A' and resid 779 through 780 Processing sheet with id= 25, first strand: chain 'A' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR A 880 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 850 " --> pdb=" O TYR A 880 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP A 882 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE A1075 " --> pdb=" O ILE A1086 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A1083 " --> pdb=" O ILE A1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1087 " --> pdb=" O GLY A1112 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY A1112 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 1129 through 1130 Processing sheet with id= 28, first strand: chain 'A' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER A1213 " --> pdb=" O CYS A1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A1205 " --> pdb=" O PHE A1211 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE A1211 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'A' and resid 1248 through 1249 Processing sheet with id= 30, first strand: chain 'A' and resid 1286 through 1288 removed outlier: 3.850A pdb=" N SER A1281 " --> pdb=" O ILE A1288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A1359 " --> pdb=" O TRP A1282 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE C 164 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 110 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP C 166 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL C 108 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS C 168 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU C 106 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG C 170 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 102 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE C 104 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU C 106 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 92 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 71 through 75 removed outlier: 7.034A pdb=" N ILE D 164 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 110 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP D 166 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL D 108 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS D 168 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU D 106 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG D 170 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE D 104 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU D 106 " --> pdb=" O ILE D 117 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE E1370 " --> pdb=" O PHE E1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE E1272 " --> pdb=" O PHE E1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E1325 " --> pdb=" O LYS E1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E1322 " --> pdb=" O ILE E1325 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE E1370 " --> pdb=" O PHE E1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE E1272 " --> pdb=" O PHE E1370 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE E1256 " --> pdb=" O MET E1352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E1348 " --> pdb=" O PHE E1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E1346 " --> pdb=" O ALA E1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E1307 " --> pdb=" O LEU E1296 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'E' and resid 33 through 34 Processing sheet with id= 37, first strand: chain 'E' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET E1238 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA E1222 " --> pdb=" O PHE E1233 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'E' and resid 71 through 73 removed outlier: 7.035A pdb=" N PHE E 84 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE E 108 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 94 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE E 106 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU E 96 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'E' and resid 121 through 126 Processing sheet with id= 40, first strand: chain 'E' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER E 226 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLY E 180 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR E 224 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE E 229 " --> pdb=" O ASP E 274 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG E 205 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY E 185 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG E 205 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 194 " --> pdb=" O PHE E 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE E 242 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 263 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER E 247 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS E 261 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS E 249 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL E 259 " --> pdb=" O HIS E 249 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'E' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE E 308 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 301 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR E 299 " --> pdb=" O GLY E 310 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'E' and resid 295 through 296 removed outlier: 7.545A pdb=" N SER E1031 " --> pdb=" O ASN E 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR E 313 " --> pdb=" O PRO E1029 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'E' and resid 332 through 338 removed outlier: 3.511A pdb=" N LYS E 404 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'E' and resid 332 through 338 Processing sheet with id= 47, first strand: chain 'E' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY E 395 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 376 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E 439 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'E' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY E 395 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 376 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN E 439 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'E' and resid 582 through 584 removed outlier: 6.493A pdb=" N THR E 582 " --> pdb=" O SER E 731 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER E 731 " --> pdb=" O THR E 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 837 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN E 563 " --> pdb=" O CYS E 461 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N CYS E 461 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL E 565 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ILE E 459 " --> pdb=" O VAL E 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET E 567 " --> pdb=" O GLN E 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN E 457 " --> pdb=" O MET E 567 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU E 899 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN E 457 " --> pdb=" O ALA E 897 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA E 897 " --> pdb=" O GLN E 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU E 896 " --> pdb=" O ILE E 591 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'E' and resid 539 through 540 Processing sheet with id= 51, first strand: chain 'E' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN E 703 " --> pdb=" O HIS E 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR E 597 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA E 701 " --> pdb=" O THR E 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR E 599 " --> pdb=" O LYS E 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS E 699 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET E 971 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN E 703 " --> pdb=" O MET E 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU E 973 " --> pdb=" O GLN E 703 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP E 966 " --> pdb=" O ARG E 952 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'E' and resid 602 through 607 removed outlier: 6.653A pdb=" N ASP E 602 " --> pdb=" O ILE E 695 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE E 695 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER E 604 " --> pdb=" O LYS E 693 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS E 693 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE E 606 " --> pdb=" O GLN E 691 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER E 963 " --> pdb=" O GLN E 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS E 693 " --> pdb=" O SER E 963 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'E' and resid 642 through 645 removed outlier: 3.519A pdb=" N GLY E 642 " --> pdb=" O VAL E 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 644 " --> pdb=" O TRP E 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP E 664 " --> pdb=" O PHE E 644 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 737 through 739 Processing sheet with id= 55, first strand: chain 'E' and resid 776 through 777 Processing sheet with id= 56, first strand: chain 'E' and resid 779 through 780 Processing sheet with id= 57, first strand: chain 'E' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR E 880 " --> pdb=" O LEU E 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU E 850 " --> pdb=" O TYR E 880 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP E 882 " --> pdb=" O LEU E 850 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'E' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE E1075 " --> pdb=" O ILE E1086 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU E1083 " --> pdb=" O ILE E1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E1087 " --> pdb=" O GLY E1112 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY E1112 " --> pdb=" O LEU E1087 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'E' and resid 1129 through 1130 Processing sheet with id= 60, first strand: chain 'E' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER E1213 " --> pdb=" O CYS E1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER E1205 " --> pdb=" O PHE E1211 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE E1211 " --> pdb=" O SER E1205 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'E' and resid 1248 through 1249 Processing sheet with id= 62, first strand: chain 'E' and resid 1286 through 1288 removed outlier: 3.849A pdb=" N SER E1281 " --> pdb=" O ILE E1288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E1359 " --> pdb=" O TRP E1282 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'G' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE G 164 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR G 110 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP G 166 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL G 108 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS G 168 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU G 106 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG G 170 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 102 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N ILE G 104 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU G 106 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 92 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'H' and resid 71 through 75 removed outlier: 7.035A pdb=" N ILE H 164 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR H 110 " --> pdb=" O ILE H 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP H 166 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL H 108 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS H 168 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU H 106 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG H 170 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE H 104 " --> pdb=" O PRO H 119 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU H 106 " --> pdb=" O ILE H 117 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.950A pdb=" N PHE I1370 " --> pdb=" O PHE I1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE I1272 " --> pdb=" O PHE I1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE I1325 " --> pdb=" O LYS I1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS I1322 " --> pdb=" O ILE I1325 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.950A pdb=" N PHE I1370 " --> pdb=" O PHE I1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE I1272 " --> pdb=" O PHE I1370 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'I' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE I1256 " --> pdb=" O MET I1352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I1348 " --> pdb=" O PHE I1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA I1346 " --> pdb=" O ALA I1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR I1307 " --> pdb=" O LEU I1296 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'I' and resid 33 through 34 Processing sheet with id= 69, first strand: chain 'I' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET I1238 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA I1222 " --> pdb=" O PHE I1233 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'I' and resid 71 through 73 removed outlier: 7.035A pdb=" N PHE I 84 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE I 108 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG I 94 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE I 106 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU I 96 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR I 104 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'I' and resid 121 through 126 Processing sheet with id= 72, first strand: chain 'I' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER I 226 " --> pdb=" O GLY I 178 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N GLY I 180 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR I 224 " --> pdb=" O GLY I 180 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE I 229 " --> pdb=" O ASP I 274 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'I' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG I 205 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY I 185 " --> pdb=" O ILE I 212 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'I' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG I 205 " --> pdb=" O PHE I 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR I 194 " --> pdb=" O PHE I 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE I 242 " --> pdb=" O TYR I 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA I 263 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER I 247 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS I 261 " --> pdb=" O SER I 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS I 249 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL I 259 " --> pdb=" O HIS I 249 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'I' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE I 308 " --> pdb=" O THR I 301 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR I 301 " --> pdb=" O PHE I 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR I 299 " --> pdb=" O GLY I 310 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'I' and resid 295 through 296 removed outlier: 7.545A pdb=" N SER I1031 " --> pdb=" O ASN I 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR I 313 " --> pdb=" O PRO I1029 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'I' and resid 332 through 338 removed outlier: 3.511A pdb=" N LYS I 404 " --> pdb=" O LEU I 415 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'I' and resid 332 through 338 Processing sheet with id= 79, first strand: chain 'I' and resid 395 through 398 removed outlier: 4.220A pdb=" N GLY I 395 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG I 376 " --> pdb=" O VAL I 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN I 439 " --> pdb=" O GLN I 382 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'I' and resid 395 through 398 removed outlier: 4.220A pdb=" N GLY I 395 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG I 376 " --> pdb=" O VAL I 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN I 439 " --> pdb=" O GLN I 382 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'I' and resid 582 through 584 removed outlier: 6.492A pdb=" N THR I 582 " --> pdb=" O SER I 731 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER I 731 " --> pdb=" O THR I 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE I 837 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN I 563 " --> pdb=" O CYS I 461 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N CYS I 461 " --> pdb=" O ASN I 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL I 565 " --> pdb=" O ILE I 459 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ILE I 459 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET I 567 " --> pdb=" O GLN I 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN I 457 " --> pdb=" O MET I 567 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU I 899 " --> pdb=" O LEU I 455 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN I 457 " --> pdb=" O ALA I 897 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA I 897 " --> pdb=" O GLN I 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU I 896 " --> pdb=" O ILE I 591 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'I' and resid 539 through 540 Processing sheet with id= 83, first strand: chain 'I' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN I 703 " --> pdb=" O HIS I 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR I 597 " --> pdb=" O ALA I 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA I 701 " --> pdb=" O THR I 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR I 599 " --> pdb=" O LYS I 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS I 699 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET I 971 " --> pdb=" O ALA I 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN I 703 " --> pdb=" O MET I 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU I 973 " --> pdb=" O GLN I 703 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP I 966 " --> pdb=" O ARG I 952 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'I' and resid 602 through 607 removed outlier: 6.654A pdb=" N ASP I 602 " --> pdb=" O ILE I 695 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE I 695 " --> pdb=" O ASP I 602 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER I 604 " --> pdb=" O LYS I 693 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS I 693 " --> pdb=" O SER I 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE I 606 " --> pdb=" O GLN I 691 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N SER I 963 " --> pdb=" O GLN I 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS I 693 " --> pdb=" O SER I 963 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'I' and resid 642 through 645 removed outlier: 3.518A pdb=" N GLY I 642 " --> pdb=" O VAL I 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE I 644 " --> pdb=" O TRP I 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP I 664 " --> pdb=" O PHE I 644 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'I' and resid 737 through 739 Processing sheet with id= 87, first strand: chain 'I' and resid 776 through 777 Processing sheet with id= 88, first strand: chain 'I' and resid 779 through 780 Processing sheet with id= 89, first strand: chain 'I' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR I 880 " --> pdb=" O LEU I 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU I 850 " --> pdb=" O TYR I 880 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP I 882 " --> pdb=" O LEU I 850 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'I' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE I1075 " --> pdb=" O ILE I1086 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU I1083 " --> pdb=" O ILE I1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU I1087 " --> pdb=" O GLY I1112 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY I1112 " --> pdb=" O LEU I1087 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'I' and resid 1129 through 1130 Processing sheet with id= 92, first strand: chain 'I' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER I1213 " --> pdb=" O CYS I1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER I1205 " --> pdb=" O PHE I1211 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE I1211 " --> pdb=" O SER I1205 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'I' and resid 1248 through 1249 Processing sheet with id= 94, first strand: chain 'I' and resid 1286 through 1288 removed outlier: 3.850A pdb=" N SER I1281 " --> pdb=" O ILE I1288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG I1359 " --> pdb=" O TRP I1282 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'K' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE K 164 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR K 110 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP K 166 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL K 108 " --> pdb=" O ASP K 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS K 168 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU K 106 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG K 170 " --> pdb=" O ILE K 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 102 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE K 104 " --> pdb=" O PRO K 119 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU K 106 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS K 92 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'L' and resid 71 through 75 removed outlier: 7.034A pdb=" N ILE L 164 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR L 110 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP L 166 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL L 108 " --> pdb=" O ASP L 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS L 168 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU L 106 " --> pdb=" O LYS L 168 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG L 170 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE L 104 " --> pdb=" O PRO L 119 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU L 106 " --> pdb=" O ILE L 117 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE M1370 " --> pdb=" O PHE M1272 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE M1272 " --> pdb=" O PHE M1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE M1325 " --> pdb=" O LYS M1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M1322 " --> pdb=" O ILE M1325 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE M1370 " --> pdb=" O PHE M1272 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE M1272 " --> pdb=" O PHE M1370 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE M1256 " --> pdb=" O MET M1352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE M1348 " --> pdb=" O PHE M1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA M1346 " --> pdb=" O ALA M1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR M1307 " --> pdb=" O LEU M1296 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'M' and resid 33 through 34 Processing sheet with id=101, first strand: chain 'M' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET M1238 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA M1222 " --> pdb=" O PHE M1233 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'M' and resid 71 through 73 removed outlier: 7.034A pdb=" N PHE M 84 " --> pdb=" O LEU M 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE M 108 " --> pdb=" O ILE M 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG M 94 " --> pdb=" O ILE M 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE M 106 " --> pdb=" O ARG M 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU M 96 " --> pdb=" O THR M 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR M 104 " --> pdb=" O GLU M 96 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'M' and resid 121 through 126 Processing sheet with id=104, first strand: chain 'M' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER M 226 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLY M 180 " --> pdb=" O THR M 224 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N THR M 224 " --> pdb=" O GLY M 180 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE M 229 " --> pdb=" O ASP M 274 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'M' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG M 205 " --> pdb=" O PHE M 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY M 185 " --> pdb=" O ILE M 212 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'M' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG M 205 " --> pdb=" O PHE M 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR M 194 " --> pdb=" O PHE M 242 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE M 242 " --> pdb=" O TYR M 194 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA M 263 " --> pdb=" O VAL M 245 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER M 247 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS M 261 " --> pdb=" O SER M 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS M 249 " --> pdb=" O VAL M 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL M 259 " --> pdb=" O HIS M 249 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'M' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE M 308 " --> pdb=" O THR M 301 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR M 301 " --> pdb=" O PHE M 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR M 299 " --> pdb=" O GLY M 310 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'M' and resid 295 through 296 removed outlier: 7.544A pdb=" N SER M1031 " --> pdb=" O ASN M 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR M 313 " --> pdb=" O PRO M1029 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'M' and resid 332 through 338 removed outlier: 3.510A pdb=" N LYS M 404 " --> pdb=" O LEU M 415 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'M' and resid 332 through 338 Processing sheet with id=111, first strand: chain 'M' and resid 395 through 398 removed outlier: 4.218A pdb=" N GLY M 395 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG M 376 " --> pdb=" O VAL M 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN M 439 " --> pdb=" O GLN M 382 " (cutoff:3.500A) Processing sheet with id=112, first strand: chain 'M' and resid 395 through 398 removed outlier: 4.218A pdb=" N GLY M 395 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG M 376 " --> pdb=" O VAL M 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN M 439 " --> pdb=" O GLN M 382 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'M' and resid 582 through 584 removed outlier: 6.492A pdb=" N THR M 582 " --> pdb=" O SER M 731 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER M 731 " --> pdb=" O THR M 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE M 837 " --> pdb=" O VAL M 565 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN M 563 " --> pdb=" O CYS M 461 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N CYS M 461 " --> pdb=" O ASN M 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL M 565 " --> pdb=" O ILE M 459 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N ILE M 459 " --> pdb=" O VAL M 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET M 567 " --> pdb=" O GLN M 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN M 457 " --> pdb=" O MET M 567 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU M 899 " --> pdb=" O LEU M 455 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN M 457 " --> pdb=" O ALA M 897 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA M 897 " --> pdb=" O GLN M 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 896 " --> pdb=" O ILE M 591 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'M' and resid 539 through 540 Processing sheet with id=115, first strand: chain 'M' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN M 703 " --> pdb=" O HIS M 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR M 597 " --> pdb=" O ALA M 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA M 701 " --> pdb=" O THR M 597 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR M 599 " --> pdb=" O LYS M 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS M 699 " --> pdb=" O THR M 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET M 971 " --> pdb=" O ALA M 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN M 703 " --> pdb=" O MET M 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU M 973 " --> pdb=" O GLN M 703 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP M 966 " --> pdb=" O ARG M 952 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'M' and resid 602 through 607 removed outlier: 6.654A pdb=" N ASP M 602 " --> pdb=" O ILE M 695 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE M 695 " --> pdb=" O ASP M 602 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER M 604 " --> pdb=" O LYS M 693 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS M 693 " --> pdb=" O SER M 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE M 606 " --> pdb=" O GLN M 691 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER M 963 " --> pdb=" O GLN M 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS M 693 " --> pdb=" O SER M 963 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'M' and resid 642 through 645 removed outlier: 3.519A pdb=" N GLY M 642 " --> pdb=" O VAL M 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE M 644 " --> pdb=" O TRP M 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP M 664 " --> pdb=" O PHE M 644 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'M' and resid 737 through 739 Processing sheet with id=119, first strand: chain 'M' and resid 776 through 777 Processing sheet with id=120, first strand: chain 'M' and resid 779 through 780 Processing sheet with id=121, first strand: chain 'M' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR M 880 " --> pdb=" O LEU M 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU M 850 " --> pdb=" O TYR M 880 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP M 882 " --> pdb=" O LEU M 850 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'M' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE M1075 " --> pdb=" O ILE M1086 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU M1083 " --> pdb=" O ILE M1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU M1087 " --> pdb=" O GLY M1112 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY M1112 " --> pdb=" O LEU M1087 " (cutoff:3.500A) Processing sheet with id=123, first strand: chain 'M' and resid 1129 through 1130 Processing sheet with id=124, first strand: chain 'M' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER M1213 " --> pdb=" O CYS M1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER M1205 " --> pdb=" O PHE M1211 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE M1211 " --> pdb=" O SER M1205 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 'M' and resid 1248 through 1249 Processing sheet with id=126, first strand: chain 'M' and resid 1286 through 1288 removed outlier: 3.850A pdb=" N SER M1281 " --> pdb=" O ILE M1288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG M1359 " --> pdb=" O TRP M1282 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'O' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE O 164 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR O 110 " --> pdb=" O ILE O 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP O 166 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL O 108 " --> pdb=" O ASP O 166 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS O 168 " --> pdb=" O GLU O 106 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU O 106 " --> pdb=" O LYS O 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG O 170 " --> pdb=" O ILE O 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU O 102 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE O 104 " --> pdb=" O PRO O 119 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU O 106 " --> pdb=" O ILE O 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS O 92 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'P' and resid 71 through 75 removed outlier: 7.034A pdb=" N ILE P 164 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR P 110 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP P 166 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL P 108 " --> pdb=" O ASP P 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS P 168 " --> pdb=" O GLU P 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU P 106 " --> pdb=" O LYS P 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG P 170 " --> pdb=" O ILE P 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE P 104 " --> pdb=" O PRO P 119 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU P 106 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'Q' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE Q1370 " --> pdb=" O PHE Q1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE Q1272 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE Q1325 " --> pdb=" O LYS Q1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS Q1322 " --> pdb=" O ILE Q1325 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'Q' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE Q1370 " --> pdb=" O PHE Q1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE Q1272 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) Processing sheet with id=131, first strand: chain 'Q' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE Q1256 " --> pdb=" O MET Q1352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE Q1348 " --> pdb=" O PHE Q1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA Q1346 " --> pdb=" O ALA Q1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR Q1307 " --> pdb=" O LEU Q1296 " (cutoff:3.500A) Processing sheet with id=132, first strand: chain 'Q' and resid 33 through 34 Processing sheet with id=133, first strand: chain 'Q' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET Q1238 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA Q1222 " --> pdb=" O PHE Q1233 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'Q' and resid 71 through 73 removed outlier: 7.034A pdb=" N PHE Q 84 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE Q 108 " --> pdb=" O ILE Q 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG Q 94 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE Q 106 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU Q 96 " --> pdb=" O THR Q 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR Q 104 " --> pdb=" O GLU Q 96 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'Q' and resid 121 through 126 Processing sheet with id=136, first strand: chain 'Q' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER Q 226 " --> pdb=" O GLY Q 178 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLY Q 180 " --> pdb=" O THR Q 224 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR Q 224 " --> pdb=" O GLY Q 180 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE Q 229 " --> pdb=" O ASP Q 274 " (cutoff:3.500A) Processing sheet with id=137, first strand: chain 'Q' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG Q 205 " --> pdb=" O PHE Q 191 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY Q 185 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'Q' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG Q 205 " --> pdb=" O PHE Q 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR Q 194 " --> pdb=" O PHE Q 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE Q 242 " --> pdb=" O TYR Q 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA Q 263 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER Q 247 " --> pdb=" O LYS Q 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS Q 261 " --> pdb=" O SER Q 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS Q 249 " --> pdb=" O VAL Q 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL Q 259 " --> pdb=" O HIS Q 249 " (cutoff:3.500A) Processing sheet with id=139, first strand: chain 'Q' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE Q 308 " --> pdb=" O THR Q 301 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR Q 301 " --> pdb=" O PHE Q 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR Q 299 " --> pdb=" O GLY Q 310 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'Q' and resid 295 through 296 removed outlier: 7.545A pdb=" N SER Q1031 " --> pdb=" O ASN Q 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR Q 313 " --> pdb=" O PRO Q1029 " (cutoff:3.500A) Processing sheet with id=141, first strand: chain 'Q' and resid 332 through 338 removed outlier: 3.511A pdb=" N LYS Q 404 " --> pdb=" O LEU Q 415 " (cutoff:3.500A) Processing sheet with id=142, first strand: chain 'Q' and resid 332 through 338 Processing sheet with id=143, first strand: chain 'Q' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY Q 395 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 376 " --> pdb=" O VAL Q 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN Q 439 " --> pdb=" O GLN Q 382 " (cutoff:3.500A) Processing sheet with id=144, first strand: chain 'Q' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY Q 395 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Q 376 " --> pdb=" O VAL Q 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN Q 439 " --> pdb=" O GLN Q 382 " (cutoff:3.500A) Processing sheet with id=145, first strand: chain 'Q' and resid 582 through 584 removed outlier: 6.493A pdb=" N THR Q 582 " --> pdb=" O SER Q 731 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER Q 731 " --> pdb=" O THR Q 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE Q 837 " --> pdb=" O VAL Q 565 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN Q 563 " --> pdb=" O CYS Q 461 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N CYS Q 461 " --> pdb=" O ASN Q 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL Q 565 " --> pdb=" O ILE Q 459 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ILE Q 459 " --> pdb=" O VAL Q 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET Q 567 " --> pdb=" O GLN Q 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN Q 457 " --> pdb=" O MET Q 567 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU Q 899 " --> pdb=" O LEU Q 455 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN Q 457 " --> pdb=" O ALA Q 897 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA Q 897 " --> pdb=" O GLN Q 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU Q 896 " --> pdb=" O ILE Q 591 " (cutoff:3.500A) Processing sheet with id=146, first strand: chain 'Q' and resid 539 through 540 Processing sheet with id=147, first strand: chain 'Q' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN Q 703 " --> pdb=" O HIS Q 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR Q 597 " --> pdb=" O ALA Q 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA Q 701 " --> pdb=" O THR Q 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR Q 599 " --> pdb=" O LYS Q 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS Q 699 " --> pdb=" O THR Q 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET Q 971 " --> pdb=" O ALA Q 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN Q 703 " --> pdb=" O MET Q 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU Q 973 " --> pdb=" O GLN Q 703 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP Q 966 " --> pdb=" O ARG Q 952 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'Q' and resid 602 through 607 removed outlier: 6.653A pdb=" N ASP Q 602 " --> pdb=" O ILE Q 695 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE Q 695 " --> pdb=" O ASP Q 602 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER Q 604 " --> pdb=" O LYS Q 693 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS Q 693 " --> pdb=" O SER Q 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE Q 606 " --> pdb=" O GLN Q 691 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER Q 963 " --> pdb=" O GLN Q 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS Q 693 " --> pdb=" O SER Q 963 " (cutoff:3.500A) Processing sheet with id=149, first strand: chain 'Q' and resid 642 through 645 removed outlier: 3.519A pdb=" N GLY Q 642 " --> pdb=" O VAL Q 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE Q 644 " --> pdb=" O TRP Q 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP Q 664 " --> pdb=" O PHE Q 644 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'Q' and resid 737 through 739 Processing sheet with id=151, first strand: chain 'Q' and resid 776 through 777 Processing sheet with id=152, first strand: chain 'Q' and resid 779 through 780 Processing sheet with id=153, first strand: chain 'Q' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR Q 880 " --> pdb=" O LEU Q 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU Q 850 " --> pdb=" O TYR Q 880 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP Q 882 " --> pdb=" O LEU Q 850 " (cutoff:3.500A) Processing sheet with id=154, first strand: chain 'Q' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE Q1075 " --> pdb=" O ILE Q1086 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU Q1083 " --> pdb=" O ILE Q1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU Q1087 " --> pdb=" O GLY Q1112 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY Q1112 " --> pdb=" O LEU Q1087 " (cutoff:3.500A) Processing sheet with id=155, first strand: chain 'Q' and resid 1129 through 1130 Processing sheet with id=156, first strand: chain 'Q' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER Q1213 " --> pdb=" O CYS Q1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER Q1205 " --> pdb=" O PHE Q1211 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE Q1211 " --> pdb=" O SER Q1205 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'Q' and resid 1248 through 1249 Processing sheet with id=158, first strand: chain 'Q' and resid 1286 through 1288 removed outlier: 3.849A pdb=" N SER Q1281 " --> pdb=" O ILE Q1288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Q1359 " --> pdb=" O TRP Q1282 " (cutoff:3.500A) Processing sheet with id=159, first strand: chain 'S' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE S 164 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR S 110 " --> pdb=" O ILE S 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP S 166 " --> pdb=" O VAL S 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL S 108 " --> pdb=" O ASP S 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS S 168 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU S 106 " --> pdb=" O LYS S 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG S 170 " --> pdb=" O ILE S 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU S 102 " --> pdb=" O ILE S 172 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N ILE S 104 " --> pdb=" O PRO S 119 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU S 106 " --> pdb=" O ILE S 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS S 92 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'T' and resid 71 through 75 removed outlier: 7.035A pdb=" N ILE T 164 " --> pdb=" O THR T 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR T 110 " --> pdb=" O ILE T 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP T 166 " --> pdb=" O VAL T 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL T 108 " --> pdb=" O ASP T 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS T 168 " --> pdb=" O GLU T 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU T 106 " --> pdb=" O LYS T 168 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG T 170 " --> pdb=" O ILE T 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE T 104 " --> pdb=" O PRO T 119 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU T 106 " --> pdb=" O ILE T 117 " (cutoff:3.500A) Processing sheet with id=161, first strand: chain 'U' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE U1370 " --> pdb=" O PHE U1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE U1272 " --> pdb=" O PHE U1370 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE U1325 " --> pdb=" O LYS U1322 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS U1322 " --> pdb=" O ILE U1325 " (cutoff:3.500A) Processing sheet with id=162, first strand: chain 'U' and resid 4 through 8 removed outlier: 6.951A pdb=" N PHE U1370 " --> pdb=" O PHE U1272 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE U1272 " --> pdb=" O PHE U1370 " (cutoff:3.500A) Processing sheet with id=163, first strand: chain 'U' and resid 29 through 31 removed outlier: 3.572A pdb=" N PHE U1256 " --> pdb=" O MET U1352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE U1348 " --> pdb=" O PHE U1260 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA U1346 " --> pdb=" O ALA U1262 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR U1307 " --> pdb=" O LEU U1296 " (cutoff:3.500A) Processing sheet with id=164, first strand: chain 'U' and resid 33 through 34 Processing sheet with id=165, first strand: chain 'U' and resid 53 through 55 removed outlier: 4.617A pdb=" N MET U1238 " --> pdb=" O ILE U 55 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA U1222 " --> pdb=" O PHE U1233 " (cutoff:3.500A) Processing sheet with id=166, first strand: chain 'U' and resid 71 through 73 removed outlier: 7.035A pdb=" N PHE U 84 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE U 108 " --> pdb=" O ILE U 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG U 94 " --> pdb=" O ILE U 106 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE U 106 " --> pdb=" O ARG U 94 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU U 96 " --> pdb=" O THR U 104 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR U 104 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing sheet with id=167, first strand: chain 'U' and resid 121 through 126 Processing sheet with id=168, first strand: chain 'U' and resid 170 through 183 removed outlier: 6.434A pdb=" N SER U 226 " --> pdb=" O GLY U 178 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N GLY U 180 " --> pdb=" O THR U 224 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N THR U 224 " --> pdb=" O GLY U 180 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE U 229 " --> pdb=" O ASP U 274 " (cutoff:3.500A) Processing sheet with id=169, first strand: chain 'U' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG U 205 " --> pdb=" O PHE U 191 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY U 185 " --> pdb=" O ILE U 212 " (cutoff:3.500A) Processing sheet with id=170, first strand: chain 'U' and resid 205 through 206 removed outlier: 4.199A pdb=" N ARG U 205 " --> pdb=" O PHE U 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR U 194 " --> pdb=" O PHE U 242 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE U 242 " --> pdb=" O TYR U 194 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA U 263 " --> pdb=" O VAL U 245 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER U 247 " --> pdb=" O LYS U 261 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS U 261 " --> pdb=" O SER U 247 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS U 249 " --> pdb=" O VAL U 259 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL U 259 " --> pdb=" O HIS U 249 " (cutoff:3.500A) Processing sheet with id=171, first strand: chain 'U' and resid 295 through 296 removed outlier: 3.833A pdb=" N PHE U 308 " --> pdb=" O THR U 301 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR U 301 " --> pdb=" O PHE U 308 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR U 299 " --> pdb=" O GLY U 310 " (cutoff:3.500A) Processing sheet with id=172, first strand: chain 'U' and resid 295 through 296 removed outlier: 7.545A pdb=" N SER U1031 " --> pdb=" O ASN U 311 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR U 313 " --> pdb=" O PRO U1029 " (cutoff:3.500A) Processing sheet with id=173, first strand: chain 'U' and resid 332 through 338 removed outlier: 3.511A pdb=" N LYS U 404 " --> pdb=" O LEU U 415 " (cutoff:3.500A) Processing sheet with id=174, first strand: chain 'U' and resid 332 through 338 Processing sheet with id=175, first strand: chain 'U' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY U 395 " --> pdb=" O LEU U 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG U 376 " --> pdb=" O VAL U 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN U 439 " --> pdb=" O GLN U 382 " (cutoff:3.500A) Processing sheet with id=176, first strand: chain 'U' and resid 395 through 398 removed outlier: 4.219A pdb=" N GLY U 395 " --> pdb=" O LEU U 377 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG U 376 " --> pdb=" O VAL U 445 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN U 439 " --> pdb=" O GLN U 382 " (cutoff:3.500A) Processing sheet with id=177, first strand: chain 'U' and resid 582 through 584 removed outlier: 6.492A pdb=" N THR U 582 " --> pdb=" O SER U 731 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N SER U 731 " --> pdb=" O THR U 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE U 837 " --> pdb=" O VAL U 565 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASN U 563 " --> pdb=" O CYS U 461 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N CYS U 461 " --> pdb=" O ASN U 563 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N VAL U 565 " --> pdb=" O ILE U 459 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ILE U 459 " --> pdb=" O VAL U 565 " (cutoff:3.500A) removed outlier: 9.231A pdb=" N MET U 567 " --> pdb=" O GLN U 457 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N GLN U 457 " --> pdb=" O MET U 567 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU U 899 " --> pdb=" O LEU U 455 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN U 457 " --> pdb=" O ALA U 897 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA U 897 " --> pdb=" O GLN U 457 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU U 896 " --> pdb=" O ILE U 591 " (cutoff:3.500A) Processing sheet with id=178, first strand: chain 'U' and resid 539 through 540 Processing sheet with id=179, first strand: chain 'U' and resid 595 through 599 removed outlier: 3.939A pdb=" N GLN U 703 " --> pdb=" O HIS U 595 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR U 597 " --> pdb=" O ALA U 701 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA U 701 " --> pdb=" O THR U 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR U 599 " --> pdb=" O LYS U 699 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS U 699 " --> pdb=" O THR U 599 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET U 971 " --> pdb=" O ALA U 701 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN U 703 " --> pdb=" O MET U 971 " (cutoff:3.500A) removed outlier: 11.369A pdb=" N GLU U 973 " --> pdb=" O GLN U 703 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP U 966 " --> pdb=" O ARG U 952 " (cutoff:3.500A) Processing sheet with id=180, first strand: chain 'U' and resid 602 through 607 removed outlier: 6.654A pdb=" N ASP U 602 " --> pdb=" O ILE U 695 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE U 695 " --> pdb=" O ASP U 602 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER U 604 " --> pdb=" O LYS U 693 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS U 693 " --> pdb=" O SER U 604 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE U 606 " --> pdb=" O GLN U 691 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N SER U 963 " --> pdb=" O GLN U 691 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS U 693 " --> pdb=" O SER U 963 " (cutoff:3.500A) Processing sheet with id=181, first strand: chain 'U' and resid 642 through 645 removed outlier: 3.518A pdb=" N GLY U 642 " --> pdb=" O VAL U 666 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE U 644 " --> pdb=" O TRP U 664 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP U 664 " --> pdb=" O PHE U 644 " (cutoff:3.500A) Processing sheet with id=182, first strand: chain 'U' and resid 737 through 739 Processing sheet with id=183, first strand: chain 'U' and resid 776 through 777 Processing sheet with id=184, first strand: chain 'U' and resid 779 through 780 Processing sheet with id=185, first strand: chain 'U' and resid 847 through 853 removed outlier: 6.862A pdb=" N TYR U 880 " --> pdb=" O LEU U 848 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU U 850 " --> pdb=" O TYR U 880 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP U 882 " --> pdb=" O LEU U 850 " (cutoff:3.500A) Processing sheet with id=186, first strand: chain 'U' and resid 1065 through 1070 removed outlier: 4.509A pdb=" N ILE U1075 " --> pdb=" O ILE U1086 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU U1083 " --> pdb=" O ILE U1116 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU U1087 " --> pdb=" O GLY U1112 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY U1112 " --> pdb=" O LEU U1087 " (cutoff:3.500A) Processing sheet with id=187, first strand: chain 'U' and resid 1129 through 1130 Processing sheet with id=188, first strand: chain 'U' and resid 1183 through 1184 removed outlier: 4.153A pdb=" N SER U1213 " --> pdb=" O CYS U1203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER U1205 " --> pdb=" O PHE U1211 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE U1211 " --> pdb=" O SER U1205 " (cutoff:3.500A) Processing sheet with id=189, first strand: chain 'U' and resid 1248 through 1249 Processing sheet with id=190, first strand: chain 'U' and resid 1286 through 1288 removed outlier: 3.850A pdb=" N SER U1281 " --> pdb=" O ILE U1288 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG U1359 " --> pdb=" O TRP U1282 " (cutoff:3.500A) Processing sheet with id=191, first strand: chain 'W' and resid 71 through 75 removed outlier: 7.080A pdb=" N ILE W 164 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR W 110 " --> pdb=" O ILE W 164 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP W 166 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL W 108 " --> pdb=" O ASP W 166 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS W 168 " --> pdb=" O GLU W 106 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU W 106 " --> pdb=" O LYS W 168 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG W 170 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU W 102 " --> pdb=" O ILE W 172 " (cutoff:3.500A) removed outlier: 11.105A pdb=" N ILE W 104 " --> pdb=" O PRO W 119 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU W 106 " --> pdb=" O ILE W 117 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS W 92 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing sheet with id=192, first strand: chain 'X' and resid 71 through 75 removed outlier: 7.034A pdb=" N ILE X 164 " --> pdb=" O THR X 110 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR X 110 " --> pdb=" O ILE X 164 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP X 166 " --> pdb=" O VAL X 108 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL X 108 " --> pdb=" O ASP X 166 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS X 168 " --> pdb=" O GLU X 106 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU X 106 " --> pdb=" O LYS X 168 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG X 170 " --> pdb=" O ILE X 104 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ILE X 104 " --> pdb=" O PRO X 119 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU X 106 " --> pdb=" O ILE X 117 " (cutoff:3.500A) 2814 hydrogen bonds defined for protein. 7290 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: 52.17 Time building geometry restraints manager: 27.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 15138 1.29 - 1.42: 24324 1.42 - 1.55: 51064 1.55 - 1.68: 2 1.68 - 1.82: 324 Bond restraints: 90852 Sorted by residual: bond pdb=" C PRO A 475 " pdb=" O PRO A 475 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" C PRO M 475 " pdb=" O PRO M 475 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.30e-02 5.92e+03 3.12e+01 bond pdb=" C PRO E 475 " pdb=" O PRO E 475 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C PRO Q 475 " pdb=" O PRO Q 475 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C PRO U 475 " pdb=" O PRO U 475 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.30e-02 5.92e+03 3.11e+01 ... (remaining 90847 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.29: 2841 107.29 - 114.12: 49846 114.12 - 120.95: 40048 120.95 - 127.78: 29991 127.78 - 134.60: 832 Bond angle restraints: 123558 Sorted by residual: angle pdb=" C LYS Q 468 " pdb=" N ASP Q 469 " pdb=" CA ASP Q 469 " ideal model delta sigma weight residual 120.31 129.71 -9.40 1.52e+00 4.33e-01 3.82e+01 angle pdb=" C LYS E 468 " pdb=" N ASP E 469 " pdb=" CA ASP E 469 " ideal model delta sigma weight residual 120.31 129.71 -9.40 1.52e+00 4.33e-01 3.82e+01 angle pdb=" C LYS M 468 " pdb=" N ASP M 469 " pdb=" CA ASP M 469 " ideal model delta sigma weight residual 120.31 129.69 -9.38 1.52e+00 4.33e-01 3.81e+01 angle pdb=" C LYS A 468 " pdb=" N ASP A 469 " pdb=" CA ASP A 469 " ideal model delta sigma weight residual 120.31 129.69 -9.38 1.52e+00 4.33e-01 3.81e+01 angle pdb=" C LYS I 468 " pdb=" N ASP I 469 " pdb=" CA ASP I 469 " ideal model delta sigma weight residual 120.31 129.67 -9.36 1.52e+00 4.33e-01 3.80e+01 ... (remaining 123553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 48946 17.98 - 35.96: 4124 35.96 - 53.94: 678 53.94 - 71.92: 138 71.92 - 89.89: 84 Dihedral angle restraints: 53970 sinusoidal: 21312 harmonic: 32658 Sorted by residual: dihedral pdb=" CA SER Q 474 " pdb=" C SER Q 474 " pdb=" N PRO Q 475 " pdb=" CA PRO Q 475 " ideal model delta harmonic sigma weight residual 180.00 148.81 31.19 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" CA SER U 474 " pdb=" C SER U 474 " pdb=" N PRO U 475 " pdb=" CA PRO U 475 " ideal model delta harmonic sigma weight residual 180.00 148.83 31.17 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" CA SER M 474 " pdb=" C SER M 474 " pdb=" N PRO M 475 " pdb=" CA PRO M 475 " ideal model delta harmonic sigma weight residual 180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 53967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 13210 0.124 - 0.249: 374 0.249 - 0.373: 36 0.373 - 0.497: 0 0.497 - 0.621: 6 Chirality restraints: 13626 Sorted by residual: chirality pdb=" CA PRO E 475 " pdb=" N PRO E 475 " pdb=" C PRO E 475 " pdb=" CB PRO E 475 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.65e+00 chirality pdb=" CA PRO Q 475 " pdb=" N PRO Q 475 " pdb=" C PRO Q 475 " pdb=" CB PRO Q 475 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.65e+00 chirality pdb=" CA PRO U 475 " pdb=" N PRO U 475 " pdb=" C PRO U 475 " pdb=" CB PRO U 475 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.62 2.00e-01 2.50e+01 9.63e+00 ... (remaining 13623 not shown) Planarity restraints: 16110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1061 " -0.033 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C ASP A1061 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP A1061 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS A1062 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP M1061 " 0.033 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C ASP M1061 " -0.111 2.00e-02 2.50e+03 pdb=" O ASP M1061 " 0.041 2.00e-02 2.50e+03 pdb=" N LYS M1062 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E1061 " -0.033 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C ASP E1061 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP E1061 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS E1062 " -0.037 2.00e-02 2.50e+03 ... (remaining 16107 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1488 2.63 - 3.20: 79929 3.20 - 3.77: 134386 3.77 - 4.33: 205509 4.33 - 4.90: 342945 Nonbonded interactions: 764257 Sorted by model distance: nonbonded pdb=" O ASN Q 473 " pdb=" ND2 ASN Q 473 " model vdw 2.066 2.520 nonbonded pdb=" O ASN E 473 " pdb=" ND2 ASN E 473 " model vdw 2.066 2.520 nonbonded pdb=" O ASN I 473 " pdb=" ND2 ASN I 473 " model vdw 2.066 2.520 nonbonded pdb=" O ASN U 473 " pdb=" ND2 ASN U 473 " model vdw 2.066 2.520 nonbonded pdb=" O ASN M 473 " pdb=" ND2 ASN M 473 " model vdw 2.066 2.520 ... (remaining 764252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 8.390 Check model and map are aligned: 0.970 Set scattering table: 0.590 Process input model: 195.320 Find NCS groups from input model: 4.300 Set up NCS constraints: 0.680 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 214.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.078 90852 Z= 0.265 Angle : 0.708 16.880 123558 Z= 0.411 Chirality : 0.053 0.621 13626 Planarity : 0.006 0.158 16110 Dihedral : 13.989 89.895 33018 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.55 % Allowed : 0.24 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.07), residues: 10974 helix: -0.15 (0.13), residues: 1536 sheet: -1.90 (0.09), residues: 2748 loop : -1.86 (0.07), residues: 6690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 481 HIS 0.011 0.001 HIS M 670 PHE 0.020 0.001 PHE A1370 TYR 0.025 0.001 TYR Q 752 ARG 0.007 0.001 ARG U 671 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1195 time to evaluate : 7.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.7851 (ttpp) cc_final: 0.6915 (mmtt) REVERT: A 627 MET cc_start: 0.8550 (mtm) cc_final: 0.8345 (mtm) REVERT: A 676 MET cc_start: 0.8767 (ppp) cc_final: 0.7868 (ptm) REVERT: A 677 ASN cc_start: 0.8420 (p0) cc_final: 0.7933 (p0) REVERT: A 901 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (ttm170) REVERT: A 906 ASN cc_start: 0.7790 (m-40) cc_final: 0.7025 (p0) REVERT: A 1238 MET cc_start: 0.8104 (mmm) cc_final: 0.7890 (mmm) REVERT: A 1248 MET cc_start: 0.8137 (mmm) cc_final: 0.7719 (mmm) REVERT: D 18 MET cc_start: 0.7564 (mtm) cc_final: 0.6982 (mtm) REVERT: D 236 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7431 (mtp-110) REVERT: E 11 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7084 (mmtt) REVERT: E 223 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7403 (mt-10) REVERT: E 264 ASP cc_start: 0.8700 (m-30) cc_final: 0.8257 (m-30) REVERT: E 340 LEU cc_start: 0.7491 (pt) cc_final: 0.7036 (mt) REVERT: E 414 THR cc_start: 0.8881 (t) cc_final: 0.8613 (m) REVERT: E 677 ASN cc_start: 0.8428 (p0) cc_final: 0.8137 (p0) REVERT: E 1018 ILE cc_start: 0.8415 (tp) cc_final: 0.8165 (tt) REVERT: E 1027 TYR cc_start: 0.8562 (t80) cc_final: 0.8344 (t80) REVERT: E 1089 ASN cc_start: 0.8322 (t0) cc_final: 0.7807 (t0) REVERT: H 41 ILE cc_start: 0.7826 (mm) cc_final: 0.7607 (mt) REVERT: H 129 MET cc_start: 0.7076 (mmm) cc_final: 0.6691 (mmm) REVERT: I 11 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7024 (mmtt) REVERT: I 256 THR cc_start: 0.8069 (m) cc_final: 0.7777 (p) REVERT: I 264 ASP cc_start: 0.8564 (m-30) cc_final: 0.8245 (m-30) REVERT: I 340 LEU cc_start: 0.7608 (pt) cc_final: 0.7265 (mt) REVERT: I 552 ASP cc_start: 0.7762 (m-30) cc_final: 0.7326 (m-30) REVERT: I 627 MET cc_start: 0.8527 (mtm) cc_final: 0.8062 (mtm) REVERT: I 685 THR cc_start: 0.8472 (p) cc_final: 0.8272 (m) REVERT: I 901 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7948 (ttm170) REVERT: I 906 ASN cc_start: 0.8112 (m-40) cc_final: 0.7390 (p0) REVERT: I 983 ASP cc_start: 0.8655 (p0) cc_final: 0.8189 (p0) REVERT: I 989 VAL cc_start: 0.8648 (m) cc_final: 0.8354 (t) REVERT: I 1074 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7713 (mm-30) REVERT: I 1080 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7534 (mtt90) REVERT: I 1089 ASN cc_start: 0.8323 (t0) cc_final: 0.7841 (t0) REVERT: I 1323 PHE cc_start: 0.8793 (m-80) cc_final: 0.8411 (m-80) REVERT: K 186 GLU cc_start: 0.8062 (mp0) cc_final: 0.7745 (mp0) REVERT: K 231 VAL cc_start: 0.7397 (t) cc_final: 0.7110 (m) REVERT: L 41 ILE cc_start: 0.7659 (mm) cc_final: 0.7440 (mt) REVERT: L 62 LYS cc_start: 0.6268 (ttpp) cc_final: 0.5720 (tptp) REVERT: L 129 MET cc_start: 0.7149 (mmm) cc_final: 0.6816 (mmm) REVERT: M 11 LYS cc_start: 0.7831 (ttpp) cc_final: 0.6903 (mmtt) REVERT: M 414 THR cc_start: 0.9090 (t) cc_final: 0.8838 (m) REVERT: M 665 MET cc_start: 0.9081 (mmm) cc_final: 0.8797 (mmm) REVERT: M 676 MET cc_start: 0.8750 (ppp) cc_final: 0.7848 (ptm) REVERT: M 677 ASN cc_start: 0.8413 (p0) cc_final: 0.7930 (p0) REVERT: M 1089 ASN cc_start: 0.8548 (t0) cc_final: 0.7954 (t0) REVERT: M 1238 MET cc_start: 0.8098 (mmm) cc_final: 0.7868 (mmm) REVERT: M 1248 MET cc_start: 0.8137 (mmm) cc_final: 0.7791 (mmm) REVERT: P 18 MET cc_start: 0.7487 (mtm) cc_final: 0.6960 (mtm) REVERT: Q 11 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7096 (mmtt) REVERT: Q 223 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7419 (mt-10) REVERT: Q 264 ASP cc_start: 0.8697 (m-30) cc_final: 0.8234 (m-30) REVERT: Q 340 LEU cc_start: 0.7454 (pt) cc_final: 0.7072 (mt) REVERT: Q 414 THR cc_start: 0.8782 (t) cc_final: 0.8538 (m) REVERT: Q 677 ASN cc_start: 0.8441 (p0) cc_final: 0.8130 (p0) REVERT: Q 771 ILE cc_start: 0.9293 (tp) cc_final: 0.9062 (tt) REVERT: Q 1018 ILE cc_start: 0.8473 (tp) cc_final: 0.8200 (tt) REVERT: Q 1027 TYR cc_start: 0.8597 (t80) cc_final: 0.8382 (t80) REVERT: Q 1089 ASN cc_start: 0.8315 (t0) cc_final: 0.7828 (t0) REVERT: T 41 ILE cc_start: 0.7823 (mm) cc_final: 0.7588 (mt) REVERT: T 129 MET cc_start: 0.7092 (mmm) cc_final: 0.6690 (mmm) REVERT: U 11 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7046 (mmtt) REVERT: U 256 THR cc_start: 0.8035 (m) cc_final: 0.7783 (p) REVERT: U 264 ASP cc_start: 0.8546 (m-30) cc_final: 0.8247 (m-30) REVERT: U 277 THR cc_start: 0.7471 (p) cc_final: 0.7185 (p) REVERT: U 340 LEU cc_start: 0.7605 (pt) cc_final: 0.7300 (mt) REVERT: U 552 ASP cc_start: 0.7753 (m-30) cc_final: 0.7301 (m-30) REVERT: U 580 ASN cc_start: 0.7894 (m-40) cc_final: 0.7687 (m110) REVERT: U 627 MET cc_start: 0.8525 (mtm) cc_final: 0.8070 (mtm) REVERT: U 901 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7962 (ttm170) REVERT: U 989 VAL cc_start: 0.8659 (m) cc_final: 0.8369 (t) REVERT: U 1074 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7718 (mm-30) REVERT: U 1080 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7538 (mtt90) REVERT: U 1089 ASN cc_start: 0.8313 (t0) cc_final: 0.7825 (t0) REVERT: U 1323 PHE cc_start: 0.8785 (m-80) cc_final: 0.8405 (m-80) REVERT: X 41 ILE cc_start: 0.7686 (mm) cc_final: 0.7389 (mt) REVERT: X 99 ASP cc_start: 0.8580 (p0) cc_final: 0.8093 (p0) REVERT: X 129 MET cc_start: 0.7058 (mmm) cc_final: 0.6686 (mmm) outliers start: 54 outliers final: 23 residues processed: 1243 average time/residue: 0.9222 time to fit residues: 2003.7857 Evaluate side-chains 807 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 781 time to evaluate : 7.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 481 TRP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 901 ARG Chi-restraints excluded: chain E residue 478 GLN Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 481 TRP Chi-restraints excluded: chain E residue 483 SER Chi-restraints excluded: chain E residue 751 ASN Chi-restraints excluded: chain I residue 480 SER Chi-restraints excluded: chain I residue 481 TRP Chi-restraints excluded: chain I residue 751 ASN Chi-restraints excluded: chain I residue 901 ARG Chi-restraints excluded: chain M residue 480 SER Chi-restraints excluded: chain M residue 481 TRP Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 751 ASN Chi-restraints excluded: chain Q residue 478 GLN Chi-restraints excluded: chain Q residue 480 SER Chi-restraints excluded: chain Q residue 481 TRP Chi-restraints excluded: chain Q residue 751 ASN Chi-restraints excluded: chain U residue 480 SER Chi-restraints excluded: chain U residue 481 TRP Chi-restraints excluded: chain U residue 751 ASN Chi-restraints excluded: chain U residue 901 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 927 optimal weight: 2.9990 chunk 832 optimal weight: 0.9990 chunk 461 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 561 optimal weight: 4.9990 chunk 444 optimal weight: 9.9990 chunk 860 optimal weight: 2.9990 chunk 333 optimal weight: 0.0980 chunk 523 optimal weight: 6.9990 chunk 640 optimal weight: 0.8980 chunk 997 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 141 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 430 GLN A 478 GLN A 568 HIS A 628 ASN A 751 ASN A 767 GLN A 919 ASN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1180 ASN A1286 ASN ** A1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 HIS C 79 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 GLN E 48 ASN E 75 ASN E 91 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 478 GLN E 568 HIS E 751 ASN E 767 GLN E 919 ASN ** E 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN E1180 ASN ** E1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1191 ASN E1247 ASN ** E1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1363 HIS G 79 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 GLN I 48 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN I 568 HIS I 751 ASN I 767 GLN I 919 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN I1124 ASN I1180 ASN I1189 ASN I1247 ASN I1286 ASN ** I1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1363 HIS K 79 ASN K 151 ASN M 141 ASN M 188 GLN M 478 GLN M 568 HIS M 628 ASN M 648 ASN M 751 ASN M 767 GLN M 919 ASN ** M 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1089 ASN M1180 ASN M1286 ASN ** M1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1363 HIS O 79 ASN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 GLN Q 48 ASN Q 75 ASN Q 91 ASN Q 141 ASN ** Q 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 188 GLN Q 478 GLN Q 568 HIS Q 751 ASN Q 767 GLN Q 919 ASN ** Q 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1180 ASN ** Q1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1191 ASN Q1247 ASN ** Q1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1363 HIS S 79 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 7 GLN U 48 ASN ** U 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 188 GLN U 430 GLN U 568 HIS U 751 ASN U 767 GLN U 919 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN U1124 ASN U1180 ASN U1247 ASN ** U1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1353 ASN U1363 HIS W 79 ASN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 90852 Z= 0.207 Angle : 0.526 8.264 123558 Z= 0.285 Chirality : 0.046 0.171 13626 Planarity : 0.005 0.096 16110 Dihedral : 5.037 64.633 12213 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.22 % Allowed : 5.47 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.07), residues: 10974 helix: 0.47 (0.13), residues: 1572 sheet: -1.30 (0.09), residues: 2814 loop : -1.65 (0.07), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 136 HIS 0.005 0.001 HIS Q 834 PHE 0.015 0.002 PHE A1277 TYR 0.013 0.001 TYR I 776 ARG 0.005 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 874 time to evaluate : 7.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7155 (mmtt) REVERT: A 283 ASP cc_start: 0.7210 (t0) cc_final: 0.6852 (t70) REVERT: A 665 MET cc_start: 0.9086 (mmm) cc_final: 0.8589 (mmm) REVERT: A 676 MET cc_start: 0.8387 (ppp) cc_final: 0.8156 (ptm) REVERT: A 677 ASN cc_start: 0.8620 (p0) cc_final: 0.8068 (p0) REVERT: A 906 ASN cc_start: 0.7869 (m-40) cc_final: 0.7143 (p0) REVERT: A 1061 ASP cc_start: 0.7834 (p0) cc_final: 0.7539 (p0) REVERT: A 1358 TYR cc_start: 0.8172 (m-80) cc_final: 0.7852 (m-10) REVERT: D 18 MET cc_start: 0.7710 (mtm) cc_final: 0.7331 (mtm) REVERT: D 39 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: D 145 ILE cc_start: 0.7841 (mm) cc_final: 0.7479 (mm) REVERT: D 236 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7471 (mtp-110) REVERT: E 6 GLU cc_start: 0.7954 (tp30) cc_final: 0.7452 (pt0) REVERT: E 11 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7105 (mmtt) REVERT: E 91 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7731 (m-40) REVERT: E 264 ASP cc_start: 0.8734 (m-30) cc_final: 0.8415 (m-30) REVERT: E 340 LEU cc_start: 0.7415 (pt) cc_final: 0.7191 (mt) REVERT: E 585 LYS cc_start: 0.8732 (mptt) cc_final: 0.8360 (mmtm) REVERT: E 753 TYR cc_start: 0.8709 (m-80) cc_final: 0.8348 (m-80) REVERT: E 1018 ILE cc_start: 0.8457 (tp) cc_final: 0.8174 (tt) REVERT: E 1089 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.7901 (t0) REVERT: H 18 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7127 (mtp) REVERT: H 39 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: H 129 MET cc_start: 0.7016 (mmm) cc_final: 0.6796 (mmm) REVERT: I 6 GLU cc_start: 0.7966 (tp30) cc_final: 0.7644 (pt0) REVERT: I 11 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7132 (mmtt) REVERT: I 256 THR cc_start: 0.8223 (m) cc_final: 0.7871 (p) REVERT: I 264 ASP cc_start: 0.8802 (m-30) cc_final: 0.8546 (m-30) REVERT: I 552 ASP cc_start: 0.8016 (m-30) cc_final: 0.7536 (m-30) REVERT: I 627 MET cc_start: 0.8637 (mtm) cc_final: 0.8351 (mtm) REVERT: I 638 GLN cc_start: 0.8266 (mt0) cc_final: 0.7998 (mt0) REVERT: I 685 THR cc_start: 0.8493 (p) cc_final: 0.8272 (m) REVERT: I 906 ASN cc_start: 0.8079 (m-40) cc_final: 0.7502 (p0) REVERT: I 989 VAL cc_start: 0.8712 (m) cc_final: 0.8441 (t) REVERT: I 1009 LYS cc_start: 0.8044 (mttp) cc_final: 0.7750 (mtpt) REVERT: I 1089 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7650 (t0) REVERT: I 1323 PHE cc_start: 0.8697 (m-80) cc_final: 0.8403 (m-80) REVERT: L 138 LYS cc_start: 0.5258 (mptt) cc_final: 0.5037 (mmtm) REVERT: M 11 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7151 (mmtt) REVERT: M 665 MET cc_start: 0.9130 (mmm) cc_final: 0.8837 (mmm) REVERT: M 676 MET cc_start: 0.8386 (ppp) cc_final: 0.8161 (ptm) REVERT: M 677 ASN cc_start: 0.8612 (p0) cc_final: 0.8044 (p0) REVERT: M 1009 LYS cc_start: 0.8343 (mttp) cc_final: 0.8038 (mtpt) REVERT: M 1061 ASP cc_start: 0.7837 (p0) cc_final: 0.7345 (t0) REVERT: M 1358 TYR cc_start: 0.8158 (m-80) cc_final: 0.7817 (m-10) REVERT: P 18 MET cc_start: 0.7674 (mtm) cc_final: 0.7333 (mtm) REVERT: P 39 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: P 145 ILE cc_start: 0.7849 (mm) cc_final: 0.7462 (mm) REVERT: P 232 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5914 (mm-30) REVERT: Q 6 GLU cc_start: 0.7955 (tp30) cc_final: 0.7452 (pt0) REVERT: Q 11 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7140 (mptt) REVERT: Q 91 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7725 (m-40) REVERT: Q 264 ASP cc_start: 0.8712 (m-30) cc_final: 0.8391 (m-30) REVERT: Q 753 TYR cc_start: 0.8700 (m-80) cc_final: 0.8339 (m-80) REVERT: Q 771 ILE cc_start: 0.9204 (tp) cc_final: 0.8987 (tt) REVERT: Q 1018 ILE cc_start: 0.8571 (tp) cc_final: 0.8222 (tt) REVERT: Q 1061 ASP cc_start: 0.7907 (p0) cc_final: 0.7116 (t0) REVERT: Q 1089 ASN cc_start: 0.8479 (t0) cc_final: 0.7966 (t0) REVERT: T 39 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: T 129 MET cc_start: 0.7004 (mmm) cc_final: 0.6797 (mmm) REVERT: U 6 GLU cc_start: 0.7980 (tp30) cc_final: 0.7646 (pt0) REVERT: U 11 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7169 (mmtt) REVERT: U 256 THR cc_start: 0.8200 (m) cc_final: 0.7874 (p) REVERT: U 264 ASP cc_start: 0.8805 (m-30) cc_final: 0.8575 (m-30) REVERT: U 552 ASP cc_start: 0.7929 (m-30) cc_final: 0.7418 (m-30) REVERT: U 567 MET cc_start: 0.8485 (ttm) cc_final: 0.8279 (ttm) REVERT: U 589 ARG cc_start: 0.8528 (ptt180) cc_final: 0.8249 (ptt180) REVERT: U 627 MET cc_start: 0.8645 (mtm) cc_final: 0.8364 (mtm) REVERT: U 638 GLN cc_start: 0.8279 (mt0) cc_final: 0.7978 (mt0) REVERT: U 989 VAL cc_start: 0.8722 (m) cc_final: 0.8446 (t) REVERT: U 1009 LYS cc_start: 0.7993 (mttp) cc_final: 0.7703 (mtpt) REVERT: U 1089 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7623 (t0) REVERT: U 1323 PHE cc_start: 0.8685 (m-80) cc_final: 0.8338 (m-80) outliers start: 120 outliers final: 83 residues processed: 955 average time/residue: 0.8099 time to fit residues: 1354.8031 Evaluate side-chains 832 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 739 time to evaluate : 7.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain E residue 48 ASN Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1290 ASN Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 926 ASP Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1290 ASN Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 604 SER Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 759 VAL Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1119 THR Chi-restraints excluded: chain M residue 1142 THR Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1212 THR Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain Q residue 48 ASN Chi-restraints excluded: chain Q residue 91 ASN Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 141 ASN Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1290 ASN Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 983 ASP Chi-restraints excluded: chain U residue 1014 THR Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1068 LEU Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1119 THR Chi-restraints excluded: chain U residue 1290 ASN Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 554 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 829 optimal weight: 5.9990 chunk 678 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 998 optimal weight: 5.9990 chunk 1079 optimal weight: 10.0000 chunk 889 optimal weight: 10.0000 chunk 990 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 801 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 155 ASN A 355 ASN A 430 GLN A 638 GLN A 648 ASN A 744 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1124 ASN A1191 ASN A1286 ASN A1353 ASN C 44 ASN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 91 ASN E 141 ASN E 177 ASN E 355 ASN E 946 GLN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN E1181 ASN E1268 ASN ** E1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN I 75 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 ASN ** I 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN I1241 GLN I1268 ASN I1353 ASN K 151 ASN L 224 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 141 ASN M 355 ASN M 638 GLN M 744 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 946 GLN ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1089 ASN M1124 ASN M1191 ASN M1286 ASN M1353 ASN P 224 GLN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN Q 91 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 ASN Q 177 ASN Q 355 ASN ** Q 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 998 ASN Q1049 ASN Q1089 ASN Q1181 ASN Q1268 ASN ** Q1300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 75 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN U 430 GLN ** U 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN U1241 GLN U1268 ASN U1286 ASN X 224 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 90852 Z= 0.521 Angle : 0.672 8.115 123558 Z= 0.362 Chirality : 0.051 0.186 13626 Planarity : 0.005 0.097 16110 Dihedral : 5.277 44.294 12162 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.85 % Allowed : 9.40 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.07), residues: 10974 helix: 0.55 (0.13), residues: 1530 sheet: -1.00 (0.10), residues: 2544 loop : -1.77 (0.07), residues: 6900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 136 HIS 0.007 0.002 HIS M 249 PHE 0.025 0.003 PHE U1277 TYR 0.025 0.002 TYR I1115 ARG 0.011 0.001 ARG U 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 810 time to evaluate : 7.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7212 (mmtt) REVERT: A 113 ASN cc_start: 0.8342 (t0) cc_final: 0.7693 (t0) REVERT: A 283 ASP cc_start: 0.7216 (t0) cc_final: 0.7008 (t0) REVERT: A 340 LEU cc_start: 0.7934 (pt) cc_final: 0.7392 (mm) REVERT: A 638 GLN cc_start: 0.8063 (mt0) cc_final: 0.7794 (mt0) REVERT: A 676 MET cc_start: 0.8515 (ppp) cc_final: 0.7977 (ptm) REVERT: A 1238 MET cc_start: 0.8436 (mmm) cc_final: 0.8157 (mmm) REVERT: A 1358 TYR cc_start: 0.8322 (m-80) cc_final: 0.8066 (m-10) REVERT: D 39 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: D 62 LYS cc_start: 0.6680 (ttpp) cc_final: 0.6406 (ttpp) REVERT: D 232 GLU cc_start: 0.6477 (mt-10) cc_final: 0.5804 (mm-30) REVERT: D 236 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7537 (mtm110) REVERT: E 6 GLU cc_start: 0.7938 (tp30) cc_final: 0.7459 (pt0) REVERT: E 11 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7207 (mptt) REVERT: E 254 ASP cc_start: 0.8343 (m-30) cc_final: 0.8092 (m-30) REVERT: E 315 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7735 (mtpt) REVERT: E 355 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8700 (p0) REVERT: E 411 TYR cc_start: 0.8917 (p90) cc_final: 0.8522 (p90) REVERT: E 947 ARG cc_start: 0.8840 (tpp-160) cc_final: 0.8577 (tpp-160) REVERT: E 1018 ILE cc_start: 0.8588 (tp) cc_final: 0.8201 (tt) REVERT: E 1061 ASP cc_start: 0.8045 (p0) cc_final: 0.6982 (t0) REVERT: E 1115 TYR cc_start: 0.8931 (m-80) cc_final: 0.8604 (m-80) REVERT: H 18 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7268 (mtp) REVERT: H 39 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: H 57 LEU cc_start: 0.7659 (tp) cc_final: 0.7378 (tp) REVERT: I 6 GLU cc_start: 0.7924 (tp30) cc_final: 0.7421 (pt0) REVERT: I 11 LYS cc_start: 0.8483 (ttpp) cc_final: 0.7252 (mmtt) REVERT: I 264 ASP cc_start: 0.9021 (m-30) cc_final: 0.8745 (m-30) REVERT: I 638 GLN cc_start: 0.8363 (mt0) cc_final: 0.8116 (mt0) REVERT: I 906 ASN cc_start: 0.8054 (m-40) cc_final: 0.7301 (p0) REVERT: I 1000 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8239 (m110) REVERT: I 1009 LYS cc_start: 0.8259 (mttp) cc_final: 0.8016 (mtpt) REVERT: I 1089 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7543 (t0) REVERT: I 1248 MET cc_start: 0.8449 (mmm) cc_final: 0.8228 (mmm) REVERT: I 1342 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8604 (ttt180) REVERT: K 236 ARG cc_start: 0.8157 (ptp-170) cc_final: 0.7801 (ptp-170) REVERT: L 236 ARG cc_start: 0.8240 (mtp180) cc_final: 0.8002 (mtp180) REVERT: M 11 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7197 (mmtt) REVERT: M 113 ASN cc_start: 0.8362 (t0) cc_final: 0.7786 (t0) REVERT: M 127 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7580 (mt-10) REVERT: M 638 GLN cc_start: 0.8042 (mt0) cc_final: 0.7650 (mt0) REVERT: M 676 MET cc_start: 0.8495 (ppp) cc_final: 0.7966 (ptm) REVERT: M 1061 ASP cc_start: 0.7685 (p0) cc_final: 0.7102 (t0) REVERT: M 1238 MET cc_start: 0.8422 (mmm) cc_final: 0.8135 (mmm) REVERT: M 1358 TYR cc_start: 0.8287 (m-80) cc_final: 0.8024 (m-10) REVERT: M 1364 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6719 (t0) REVERT: O 116 GLN cc_start: 0.8687 (mm110) cc_final: 0.8375 (mm-40) REVERT: P 39 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: P 62 LYS cc_start: 0.6678 (ttpp) cc_final: 0.6392 (ttpp) REVERT: P 232 GLU cc_start: 0.6438 (mt-10) cc_final: 0.5822 (mm-30) REVERT: Q 6 GLU cc_start: 0.7946 (tp30) cc_final: 0.7461 (pt0) REVERT: Q 11 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7214 (mptt) REVERT: Q 1061 ASP cc_start: 0.7995 (p0) cc_final: 0.6956 (t0) REVERT: Q 1089 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7858 (t0) REVERT: S 1 MET cc_start: 0.7044 (ptp) cc_final: 0.6746 (ptp) REVERT: T 39 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: T 57 LEU cc_start: 0.7602 (tp) cc_final: 0.7316 (tp) REVERT: U 6 GLU cc_start: 0.7927 (tp30) cc_final: 0.7429 (pt0) REVERT: U 11 LYS cc_start: 0.8500 (ttpp) cc_final: 0.7295 (mmtt) REVERT: U 264 ASP cc_start: 0.9053 (m-30) cc_final: 0.8822 (m-30) REVERT: U 1009 LYS cc_start: 0.8218 (mttp) cc_final: 0.7950 (mtpt) REVERT: U 1248 MET cc_start: 0.8487 (mmm) cc_final: 0.8254 (mmm) REVERT: W 9 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6631 (mp0) REVERT: W 236 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.5761 (mtt-85) outliers start: 182 outliers final: 140 residues processed: 935 average time/residue: 0.8250 time to fit residues: 1342.2545 Evaluate side-chains 849 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 699 time to evaluate : 7.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1268 ASN Chi-restraints excluded: chain A residue 1274 THR Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 606 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1290 ASN Chi-restraints excluded: chain E residue 1344 THR Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 606 ILE Chi-restraints excluded: chain I residue 926 ASP Chi-restraints excluded: chain I residue 1000 ASN Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1274 THR Chi-restraints excluded: chain I residue 1290 ASN Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1344 THR Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 604 SER Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 694 ILE Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 759 VAL Chi-restraints excluded: chain M residue 852 MET Chi-restraints excluded: chain M residue 926 ASP Chi-restraints excluded: chain M residue 929 ILE Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1114 ARG Chi-restraints excluded: chain M residue 1119 THR Chi-restraints excluded: chain M residue 1142 THR Chi-restraints excluded: chain M residue 1165 ILE Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1268 ASN Chi-restraints excluded: chain M residue 1274 THR Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 177 ASN Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 483 SER Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 606 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1089 ASN Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1142 THR Chi-restraints excluded: chain Q residue 1290 ASN Chi-restraints excluded: chain Q residue 1344 THR Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain T residue 161 ASN Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 426 SER Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 926 ASP Chi-restraints excluded: chain U residue 1014 THR Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1068 LEU Chi-restraints excluded: chain U residue 1119 THR Chi-restraints excluded: chain U residue 1274 THR Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1306 THR Chi-restraints excluded: chain U residue 1344 THR Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 986 optimal weight: 4.9990 chunk 751 optimal weight: 0.8980 chunk 518 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 476 optimal weight: 0.6980 chunk 670 optimal weight: 0.7980 chunk 1002 optimal weight: 5.9990 chunk 1061 optimal weight: 0.0040 chunk 523 optimal weight: 2.9990 chunk 950 optimal weight: 0.9980 chunk 286 optimal weight: 0.3980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 355 ASN A 384 ASN A 628 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1089 ASN A1329 ASN C 44 ASN C 151 ASN D 224 GLN E 52 ASN E 91 ASN E 141 ASN ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN E 473 ASN E 638 GLN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 998 ASN E1089 ASN E1124 ASN ** E1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1247 ASN E1329 ASN G 44 ASN G 151 ASN I 48 ASN I 52 ASN I 155 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 857 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN I1286 ASN K 44 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN M 384 ASN M 628 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 998 ASN M1089 ASN M1286 ASN M1329 ASN O 44 ASN O 151 ASN Q 52 ASN Q 91 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 ASN Q 638 GLN Q 946 GLN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1124 ASN ** Q1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1247 ASN ** Q1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 224 GLN U 48 ASN U 52 ASN ** U 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 638 GLN U 857 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN U1286 ASN ** U1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 90852 Z= 0.138 Angle : 0.476 7.960 123558 Z= 0.259 Chirality : 0.044 0.191 13626 Planarity : 0.004 0.072 16110 Dihedral : 4.618 49.992 12162 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.97 % Rotamer: Outliers : 1.14 % Allowed : 11.51 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.08), residues: 10974 helix: 0.99 (0.13), residues: 1584 sheet: -0.75 (0.10), residues: 2526 loop : -1.56 (0.07), residues: 6864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 136 HIS 0.004 0.001 HIS I 513 PHE 0.012 0.001 PHE M 393 TYR 0.018 0.001 TYR E 753 ARG 0.005 0.000 ARG M1114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 869 time to evaluate : 7.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7083 (mmtt) REVERT: A 113 ASN cc_start: 0.8181 (t0) cc_final: 0.7977 (t0) REVERT: A 340 LEU cc_start: 0.7533 (pt) cc_final: 0.7079 (mm) REVERT: A 676 MET cc_start: 0.8325 (ppp) cc_final: 0.8094 (ptm) REVERT: A 677 ASN cc_start: 0.8740 (p0) cc_final: 0.8167 (p0) REVERT: A 906 ASN cc_start: 0.7787 (m-40) cc_final: 0.7442 (p0) REVERT: A 946 GLN cc_start: 0.8842 (mt0) cc_final: 0.8621 (mt0) REVERT: A 1149 ASN cc_start: 0.8640 (p0) cc_final: 0.8303 (p0) REVERT: A 1238 MET cc_start: 0.8286 (mmm) cc_final: 0.7978 (mmm) REVERT: A 1241 GLN cc_start: 0.7830 (mt0) cc_final: 0.7530 (mt0) REVERT: A 1358 TYR cc_start: 0.8189 (m-80) cc_final: 0.7870 (m-10) REVERT: D 39 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: D 145 ILE cc_start: 0.7634 (mm) cc_final: 0.7428 (mm) REVERT: D 232 GLU cc_start: 0.6585 (mt-10) cc_final: 0.5933 (mm-30) REVERT: E 6 GLU cc_start: 0.7884 (tp30) cc_final: 0.7441 (pt0) REVERT: E 11 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7046 (mmtt) REVERT: E 91 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7564 (m-40) REVERT: E 138 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6700 (m-30) REVERT: E 264 ASP cc_start: 0.8956 (m-30) cc_final: 0.8659 (m-30) REVERT: E 315 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7477 (mtpt) REVERT: E 355 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8330 (p0) REVERT: E 638 GLN cc_start: 0.8006 (mt0) cc_final: 0.7774 (mt0) REVERT: E 1018 ILE cc_start: 0.8528 (tp) cc_final: 0.8206 (tt) REVERT: E 1036 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8368 (mmtm) REVERT: E 1061 ASP cc_start: 0.7940 (p0) cc_final: 0.7383 (t0) REVERT: E 1115 TYR cc_start: 0.8753 (m-80) cc_final: 0.8401 (m-80) REVERT: E 1182 TYR cc_start: 0.8487 (m-80) cc_final: 0.8191 (m-80) REVERT: G 60 SER cc_start: 0.8636 (m) cc_final: 0.8061 (p) REVERT: H 39 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: H 57 LEU cc_start: 0.7546 (tp) cc_final: 0.7261 (tp) REVERT: I 6 GLU cc_start: 0.7953 (tp30) cc_final: 0.7441 (pt0) REVERT: I 11 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7275 (mmtt) REVERT: I 340 LEU cc_start: 0.7656 (pt) cc_final: 0.7371 (pt) REVERT: I 383 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: I 906 ASN cc_start: 0.8119 (m-40) cc_final: 0.7572 (p0) REVERT: I 1009 LYS cc_start: 0.8025 (mttp) cc_final: 0.7717 (mtpt) REVERT: I 1089 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7826 (t0) REVERT: I 1157 ASP cc_start: 0.8311 (m-30) cc_final: 0.7985 (m-30) REVERT: I 1323 PHE cc_start: 0.8736 (m-80) cc_final: 0.8473 (m-80) REVERT: I 1330 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (mm) REVERT: K 186 GLU cc_start: 0.7952 (mp0) cc_final: 0.7591 (mp0) REVERT: L 236 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7937 (mtp180) REVERT: M 11 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7042 (mmtt) REVERT: M 665 MET cc_start: 0.8799 (mmm) cc_final: 0.8419 (mmm) REVERT: M 676 MET cc_start: 0.8333 (ppp) cc_final: 0.8047 (ptm) REVERT: M 677 ASN cc_start: 0.8757 (p0) cc_final: 0.8159 (p0) REVERT: M 1061 ASP cc_start: 0.7520 (p0) cc_final: 0.7054 (t0) REVERT: M 1238 MET cc_start: 0.8268 (mmm) cc_final: 0.7947 (mmm) REVERT: M 1241 GLN cc_start: 0.7817 (mt0) cc_final: 0.7514 (mt0) REVERT: M 1358 TYR cc_start: 0.8158 (m-80) cc_final: 0.7830 (m-10) REVERT: P 39 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: P 232 GLU cc_start: 0.6569 (mt-10) cc_final: 0.5943 (mm-30) REVERT: Q 6 GLU cc_start: 0.7895 (tp30) cc_final: 0.7443 (pt0) REVERT: Q 11 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7097 (mmtt) REVERT: Q 264 ASP cc_start: 0.8863 (m-30) cc_final: 0.8456 (m-30) REVERT: Q 315 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7608 (mtpt) REVERT: Q 1061 ASP cc_start: 0.7985 (p0) cc_final: 0.7343 (t0) REVERT: Q 1089 ASN cc_start: 0.8233 (t0) cc_final: 0.7766 (t0) REVERT: Q 1182 TYR cc_start: 0.8467 (m-80) cc_final: 0.8158 (m-80) REVERT: T 39 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: T 57 LEU cc_start: 0.7498 (tp) cc_final: 0.7234 (tp) REVERT: U 6 GLU cc_start: 0.7952 (tp30) cc_final: 0.7446 (pt0) REVERT: U 11 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7324 (mmtt) REVERT: U 264 ASP cc_start: 0.8889 (m-30) cc_final: 0.8674 (m-30) REVERT: U 383 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: U 533 SER cc_start: 0.8360 (m) cc_final: 0.8006 (p) REVERT: U 567 MET cc_start: 0.8466 (ttm) cc_final: 0.8234 (ttm) REVERT: U 638 GLN cc_start: 0.8143 (mt0) cc_final: 0.7911 (mt0) REVERT: U 906 ASN cc_start: 0.7883 (m-40) cc_final: 0.7276 (p0) REVERT: U 1000 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7503 (m110) REVERT: U 1009 LYS cc_start: 0.8029 (mttp) cc_final: 0.7696 (mtpt) REVERT: U 1157 ASP cc_start: 0.8267 (m-30) cc_final: 0.8008 (m-30) REVERT: U 1323 PHE cc_start: 0.8710 (m-80) cc_final: 0.8506 (m-80) REVERT: U 1330 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (mm) REVERT: W 236 ARG cc_start: 0.7770 (ptp-170) cc_final: 0.5767 (mtt-85) outliers start: 112 outliers final: 60 residues processed: 941 average time/residue: 0.8373 time to fit residues: 1377.1464 Evaluate side-chains 829 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 756 time to evaluate : 7.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1212 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 998 ASN Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 383 ASP Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1212 THR Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 383 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1130 GLU Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 883 optimal weight: 30.0000 chunk 602 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 790 optimal weight: 5.9990 chunk 437 optimal weight: 8.9990 chunk 905 optimal weight: 6.9990 chunk 733 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 541 optimal weight: 9.9990 chunk 952 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 355 ASN A 430 GLN A 628 ASN A 638 GLN A 648 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1241 GLN C 44 ASN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 91 ASN E 141 ASN E 355 ASN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 998 ASN E1089 ASN ** E1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN I 52 ASN I 155 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 ASN I 638 GLN I 744 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN K 44 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 ASN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 ASN M 355 ASN M 628 ASN M 638 GLN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1089 ASN M1241 GLN O 44 ASN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 52 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 355 ASN Q 638 GLN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1049 ASN Q1089 ASN ** Q1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1268 ASN S 44 ASN ** S 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN U 155 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN U 744 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN W 44 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 90852 Z= 0.437 Angle : 0.603 8.119 123558 Z= 0.325 Chirality : 0.049 0.186 13626 Planarity : 0.005 0.082 16110 Dihedral : 5.027 40.292 12162 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.47 % Allowed : 11.59 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.08), residues: 10974 helix: 0.78 (0.13), residues: 1578 sheet: -0.85 (0.10), residues: 2598 loop : -1.60 (0.07), residues: 6798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 136 HIS 0.005 0.001 HIS E1171 PHE 0.022 0.002 PHE I1277 TYR 0.022 0.002 TYR I1115 ARG 0.007 0.001 ARG Q 981 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 759 time to evaluate : 7.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7366 (mptt) REVERT: A 113 ASN cc_start: 0.8060 (t0) cc_final: 0.7853 (t0) REVERT: A 330 ASP cc_start: 0.7100 (m-30) cc_final: 0.6596 (m-30) REVERT: A 340 LEU cc_start: 0.7759 (pt) cc_final: 0.7206 (mm) REVERT: A 676 MET cc_start: 0.8405 (ppp) cc_final: 0.7898 (ptm) REVERT: A 1238 MET cc_start: 0.8402 (mmm) cc_final: 0.8137 (mmm) REVERT: A 1248 MET cc_start: 0.8653 (mmm) cc_final: 0.8278 (mmm) REVERT: A 1358 TYR cc_start: 0.8252 (m-80) cc_final: 0.7984 (m-10) REVERT: D 39 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: D 62 LYS cc_start: 0.6727 (ttpp) cc_final: 0.6475 (ttpp) REVERT: D 232 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6033 (mm-30) REVERT: D 238 GLU cc_start: 0.4691 (tt0) cc_final: 0.4297 (tt0) REVERT: E 6 GLU cc_start: 0.7928 (tp30) cc_final: 0.7456 (pt0) REVERT: E 11 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7204 (mptt) REVERT: E 91 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7691 (m-40) REVERT: E 254 ASP cc_start: 0.8328 (m-30) cc_final: 0.8077 (m-30) REVERT: E 315 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7533 (mtpt) REVERT: E 341 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7145 (p0) REVERT: E 1009 LYS cc_start: 0.8182 (mttp) cc_final: 0.7778 (mtpt) REVERT: E 1018 ILE cc_start: 0.8575 (tp) cc_final: 0.8179 (tt) REVERT: E 1030 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8073 (m-40) REVERT: E 1061 ASP cc_start: 0.7963 (p0) cc_final: 0.6932 (t0) REVERT: E 1115 TYR cc_start: 0.8912 (m-80) cc_final: 0.8609 (m-80) REVERT: E 1181 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8428 (m110) REVERT: H 39 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: H 57 LEU cc_start: 0.7627 (tp) cc_final: 0.7259 (tp) REVERT: I 6 GLU cc_start: 0.7988 (tp30) cc_final: 0.7478 (pt0) REVERT: I 11 LYS cc_start: 0.8460 (ttpp) cc_final: 0.7267 (mmtt) REVERT: I 316 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7896 (mtt-85) REVERT: I 340 LEU cc_start: 0.7790 (pt) cc_final: 0.7582 (pt) REVERT: I 341 ASP cc_start: 0.6694 (OUTLIER) cc_final: 0.6411 (t0) REVERT: I 455 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8267 (tp) REVERT: I 665 MET cc_start: 0.8702 (mmm) cc_final: 0.8126 (mmm) REVERT: I 901 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7442 (mtm180) REVERT: I 906 ASN cc_start: 0.8065 (m-40) cc_final: 0.7282 (p0) REVERT: I 1009 LYS cc_start: 0.8200 (mttp) cc_final: 0.7956 (mtpt) REVERT: I 1089 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7843 (t0) REVERT: I 1330 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (mm) REVERT: K 2 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7006 (p0) REVERT: K 186 GLU cc_start: 0.8071 (mp0) cc_final: 0.7694 (mp0) REVERT: K 236 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7866 (ptp-170) REVERT: M 11 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7337 (mptt) REVERT: M 330 ASP cc_start: 0.7149 (m-30) cc_final: 0.6605 (m-30) REVERT: M 665 MET cc_start: 0.8816 (mmm) cc_final: 0.8429 (mmm) REVERT: M 676 MET cc_start: 0.8381 (ppp) cc_final: 0.7858 (ptm) REVERT: M 1061 ASP cc_start: 0.7616 (p0) cc_final: 0.7108 (t0) REVERT: M 1238 MET cc_start: 0.8378 (mmm) cc_final: 0.8116 (mmm) REVERT: M 1358 TYR cc_start: 0.8229 (m-80) cc_final: 0.7968 (m-10) REVERT: M 1364 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6635 (t0) REVERT: P 39 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: P 62 LYS cc_start: 0.6702 (ttpp) cc_final: 0.6449 (ttpp) REVERT: P 232 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6052 (mm-30) REVERT: Q 6 GLU cc_start: 0.7941 (tp30) cc_final: 0.7456 (pt0) REVERT: Q 11 LYS cc_start: 0.8319 (ttpp) cc_final: 0.7206 (mptt) REVERT: Q 315 LYS cc_start: 0.8545 (mmmt) cc_final: 0.7779 (mtpt) REVERT: Q 341 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7241 (p0) REVERT: Q 1030 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: Q 1061 ASP cc_start: 0.7938 (p0) cc_final: 0.6941 (t0) REVERT: Q 1181 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8455 (m110) REVERT: T 39 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: T 57 LEU cc_start: 0.7475 (tp) cc_final: 0.7172 (tp) REVERT: U 6 GLU cc_start: 0.7991 (tp30) cc_final: 0.7490 (pt0) REVERT: U 11 LYS cc_start: 0.8469 (ttpp) cc_final: 0.7292 (mmtt) REVERT: U 264 ASP cc_start: 0.9055 (m-30) cc_final: 0.8751 (m-30) REVERT: U 316 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7860 (mtt-85) REVERT: U 455 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8285 (tp) REVERT: U 460 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8786 (mp) REVERT: U 665 MET cc_start: 0.8733 (mmm) cc_final: 0.8155 (mmm) REVERT: U 901 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7461 (mtm180) REVERT: U 1000 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8372 (m110) REVERT: U 1009 LYS cc_start: 0.8223 (mttp) cc_final: 0.7968 (mtpt) REVERT: U 1089 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7764 (t0) REVERT: U 1248 MET cc_start: 0.8618 (mmm) cc_final: 0.8403 (mmm) REVERT: U 1330 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8230 (mm) REVERT: W 2 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7003 (p0) REVERT: W 236 ARG cc_start: 0.7810 (ptp-170) cc_final: 0.5820 (mtt-85) outliers start: 243 outliers final: 166 residues processed: 933 average time/residue: 0.8321 time to fit residues: 1346.6462 Evaluate side-chains 907 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 716 time to evaluate : 7.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 926 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1114 ARG Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1030 ASN Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1181 ASN Chi-restraints excluded: chain E residue 1344 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 632 SER Chi-restraints excluded: chain I residue 703 GLN Chi-restraints excluded: chain I residue 901 ARG Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1290 ASN Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain I residue 1344 THR Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 177 ASN Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 604 SER Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 694 ILE Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 852 MET Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 926 ASP Chi-restraints excluded: chain M residue 929 ILE Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1017 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1114 ARG Chi-restraints excluded: chain M residue 1119 THR Chi-restraints excluded: chain M residue 1142 THR Chi-restraints excluded: chain M residue 1165 ILE Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 253 ILE Chi-restraints excluded: chain Q residue 341 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 663 LEU Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1030 ASN Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1142 THR Chi-restraints excluded: chain Q residue 1181 ASN Chi-restraints excluded: chain Q residue 1290 ASN Chi-restraints excluded: chain Q residue 1344 THR Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 460 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 632 SER Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 901 ARG Chi-restraints excluded: chain U residue 926 ASP Chi-restraints excluded: chain U residue 929 ILE Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1014 THR Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1068 LEU Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1096 THR Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1119 THR Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1306 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain U residue 1344 THR Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 357 optimal weight: 30.0000 chunk 955 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 623 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 1062 optimal weight: 20.0000 chunk 881 optimal weight: 0.9990 chunk 491 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 557 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 142 GLN A 355 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1089 ASN C 15 ASN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 141 ASN E 355 ASN E 638 GLN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN ** E1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1268 ASN G 44 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 GLN M 355 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 998 ASN M1089 ASN O 44 ASN ** Q 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 355 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN S 151 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 90852 Z= 0.339 Angle : 0.557 9.023 123558 Z= 0.300 Chirality : 0.047 0.185 13626 Planarity : 0.004 0.083 16110 Dihedral : 4.947 41.069 12162 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.63 % Allowed : 12.46 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.08), residues: 10974 helix: 0.84 (0.13), residues: 1578 sheet: -0.66 (0.10), residues: 2532 loop : -1.58 (0.07), residues: 6864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 136 HIS 0.004 0.001 HIS E1171 PHE 0.017 0.002 PHE U1277 TYR 0.019 0.002 TYR U 397 ARG 0.005 0.000 ARG I1342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 774 time to evaluate : 7.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7275 (mptt) REVERT: A 195 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.7930 (t0) REVERT: A 330 ASP cc_start: 0.7219 (m-30) cc_final: 0.6671 (m-30) REVERT: A 340 LEU cc_start: 0.7852 (pt) cc_final: 0.7394 (mm) REVERT: A 665 MET cc_start: 0.8682 (mmm) cc_final: 0.8198 (mmm) REVERT: A 676 MET cc_start: 0.8427 (ppp) cc_final: 0.8004 (ptm) REVERT: A 790 ILE cc_start: 0.9266 (tt) cc_final: 0.9034 (tt) REVERT: A 906 ASN cc_start: 0.7917 (m-40) cc_final: 0.7563 (p0) REVERT: A 1330 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 1358 TYR cc_start: 0.8216 (m-80) cc_final: 0.7966 (m-10) REVERT: C 2 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6666 (p0) REVERT: D 39 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: D 232 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6022 (mm-30) REVERT: E 6 GLU cc_start: 0.7890 (tp30) cc_final: 0.7440 (pt0) REVERT: E 11 LYS cc_start: 0.8354 (ttpp) cc_final: 0.7063 (mmtt) REVERT: E 91 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7698 (m-40) REVERT: E 254 ASP cc_start: 0.8317 (m-30) cc_final: 0.8063 (m-30) REVERT: E 300 MET cc_start: 0.8463 (ptt) cc_final: 0.8040 (ptp) REVERT: E 315 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7565 (mtpt) REVERT: E 341 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7107 (p0) REVERT: E 1009 LYS cc_start: 0.8152 (mttp) cc_final: 0.7789 (mtpt) REVERT: E 1018 ILE cc_start: 0.8552 (tp) cc_final: 0.8161 (tt) REVERT: E 1030 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8204 (m-40) REVERT: E 1061 ASP cc_start: 0.7890 (p0) cc_final: 0.6894 (t0) REVERT: E 1089 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8119 (t0) REVERT: E 1115 TYR cc_start: 0.8895 (m-80) cc_final: 0.8620 (m-80) REVERT: H 57 LEU cc_start: 0.7572 (tp) cc_final: 0.7275 (tp) REVERT: I 6 GLU cc_start: 0.7981 (tp30) cc_final: 0.7459 (pt0) REVERT: I 11 LYS cc_start: 0.8436 (ttpp) cc_final: 0.7264 (mmtt) REVERT: I 280 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7427 (mt-10) REVERT: I 341 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6636 (t0) REVERT: I 383 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: I 455 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8249 (tp) REVERT: I 901 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: I 906 ASN cc_start: 0.8191 (m-40) cc_final: 0.7662 (p0) REVERT: I 1000 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8134 (m110) REVERT: I 1009 LYS cc_start: 0.8208 (mttp) cc_final: 0.7877 (mtpt) REVERT: I 1089 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7783 (t0) REVERT: I 1094 ILE cc_start: 0.5194 (OUTLIER) cc_final: 0.4964 (tp) REVERT: I 1330 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8273 (mm) REVERT: K 2 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.6700 (p0) REVERT: K 186 GLU cc_start: 0.8038 (mp0) cc_final: 0.7667 (mp0) REVERT: K 236 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7761 (ptp-170) REVERT: M 11 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7241 (mptt) REVERT: M 195 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7929 (t0) REVERT: M 330 ASP cc_start: 0.7268 (m-30) cc_final: 0.6692 (m-30) REVERT: M 665 MET cc_start: 0.8827 (mmm) cc_final: 0.8399 (mmm) REVERT: M 676 MET cc_start: 0.8406 (ppp) cc_final: 0.7985 (ptm) REVERT: M 1061 ASP cc_start: 0.7626 (p0) cc_final: 0.7078 (t0) REVERT: M 1330 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8559 (mm) REVERT: M 1358 TYR cc_start: 0.8176 (m-80) cc_final: 0.7918 (m-10) REVERT: M 1364 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.6505 (t0) REVERT: O 2 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6679 (p0) REVERT: P 39 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: P 62 LYS cc_start: 0.6637 (ttpp) cc_final: 0.6387 (ttpp) REVERT: P 232 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6036 (mm-30) REVERT: Q 6 GLU cc_start: 0.7915 (tp30) cc_final: 0.7446 (pt0) REVERT: Q 11 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7033 (mmtt) REVERT: Q 315 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7638 (mtpt) REVERT: Q 1030 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8183 (m-40) REVERT: Q 1037 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: Q 1061 ASP cc_start: 0.7925 (p0) cc_final: 0.6883 (t0) REVERT: Q 1089 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8051 (t0) REVERT: S 129 MET cc_start: 0.7547 (tpp) cc_final: 0.7225 (mmp) REVERT: T 57 LEU cc_start: 0.7577 (tp) cc_final: 0.7245 (tp) REVERT: U 6 GLU cc_start: 0.7980 (tp30) cc_final: 0.7468 (pt0) REVERT: U 11 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7288 (mmtt) REVERT: U 316 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7860 (mtt-85) REVERT: U 340 LEU cc_start: 0.7866 (pt) cc_final: 0.7635 (pt) REVERT: U 383 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: U 455 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8128 (tp) REVERT: U 638 GLN cc_start: 0.8250 (mt0) cc_final: 0.7881 (mt0) REVERT: U 901 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7475 (mtm180) REVERT: U 983 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8321 (p0) REVERT: U 1000 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8038 (m110) REVERT: U 1009 LYS cc_start: 0.8194 (mttp) cc_final: 0.7930 (mtpt) REVERT: U 1089 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7814 (t0) REVERT: U 1330 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8307 (mm) REVERT: W 2 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.6994 (p0) REVERT: W 236 ARG cc_start: 0.7807 (ptp-170) cc_final: 0.5821 (mtt-85) outliers start: 259 outliers final: 175 residues processed: 964 average time/residue: 0.8288 time to fit residues: 1394.3737 Evaluate side-chains 948 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 740 time to evaluate : 7.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 341 ASP Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 514 ASN Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1030 ASN Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1096 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1142 THR Chi-restraints excluded: chain E residue 1268 ASN Chi-restraints excluded: chain E residue 1344 THR Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 341 ASP Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 632 SER Chi-restraints excluded: chain I residue 703 GLN Chi-restraints excluded: chain I residue 879 VAL Chi-restraints excluded: chain I residue 901 ARG Chi-restraints excluded: chain I residue 929 ILE Chi-restraints excluded: chain I residue 1000 ASN Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain I residue 1344 THR Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain M residue 195 ASN Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 627 MET Chi-restraints excluded: chain M residue 694 ILE Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 852 MET Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 929 ILE Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1017 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1119 THR Chi-restraints excluded: chain M residue 1165 ILE Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1330 ILE Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 253 ILE Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 514 ASN Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 663 LEU Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 960 ASP Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1030 ASN Chi-restraints excluded: chain Q residue 1037 GLU Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1089 ASN Chi-restraints excluded: chain Q residue 1096 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1142 THR Chi-restraints excluded: chain Q residue 1344 THR Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain T residue 69 GLU Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 128 ASN Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 383 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 632 SER Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 879 VAL Chi-restraints excluded: chain U residue 901 ARG Chi-restraints excluded: chain U residue 929 ILE Chi-restraints excluded: chain U residue 983 ASP Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1014 THR Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1068 LEU Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1096 THR Chi-restraints excluded: chain U residue 1113 LYS Chi-restraints excluded: chain U residue 1119 THR Chi-restraints excluded: chain U residue 1290 ASN Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1306 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain U residue 1344 THR Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 1024 optimal weight: 0.0270 chunk 119 optimal weight: 0.2980 chunk 605 optimal weight: 2.9990 chunk 775 optimal weight: 3.9990 chunk 601 optimal weight: 1.9990 chunk 894 optimal weight: 9.9990 chunk 593 optimal weight: 0.7980 chunk 1058 optimal weight: 7.9990 chunk 662 optimal weight: 0.9990 chunk 645 optimal weight: 0.9980 chunk 488 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 628 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN A1089 ASN C 15 ASN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 141 ASN E 355 ASN E 473 ASN E 638 GLN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN ** E1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1268 ASN G 44 ASN I 52 ASN I 128 ASN I 302 GLN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** I1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 628 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 998 ASN M1089 ASN O 44 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1329 ASN S 44 ASN U 52 ASN U 155 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 90852 Z= 0.141 Angle : 0.467 7.987 123558 Z= 0.252 Chirality : 0.044 0.182 13626 Planarity : 0.004 0.072 16110 Dihedral : 4.501 44.804 12162 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.50 % Favored : 95.49 % Rotamer: Outliers : 1.77 % Allowed : 13.75 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.08), residues: 10974 helix: 1.10 (0.13), residues: 1626 sheet: -0.51 (0.10), residues: 2526 loop : -1.39 (0.07), residues: 6822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 136 HIS 0.003 0.001 HIS U 513 PHE 0.031 0.001 PHE E1088 TYR 0.012 0.001 TYR E 753 ARG 0.007 0.000 ARG E1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 873 time to evaluate : 9.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8129 (ttpp) cc_final: 0.7261 (mptt) REVERT: A 315 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7950 (mtpt) REVERT: A 330 ASP cc_start: 0.7108 (m-30) cc_final: 0.6570 (m-30) REVERT: A 340 LEU cc_start: 0.7332 (pt) cc_final: 0.6906 (mm) REVERT: A 650 LYS cc_start: 0.8020 (tptt) cc_final: 0.7596 (tptm) REVERT: A 665 MET cc_start: 0.8608 (mmm) cc_final: 0.8157 (mmm) REVERT: A 676 MET cc_start: 0.8372 (ppp) cc_final: 0.8158 (ptm) REVERT: A 677 ASN cc_start: 0.8826 (p0) cc_final: 0.8327 (p0) REVERT: A 979 ASP cc_start: 0.8709 (m-30) cc_final: 0.8253 (m-30) REVERT: A 1037 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: A 1149 ASN cc_start: 0.8646 (p0) cc_final: 0.8345 (p0) REVERT: A 1241 GLN cc_start: 0.8009 (mt0) cc_final: 0.7619 (mt0) REVERT: A 1248 MET cc_start: 0.8566 (mmm) cc_final: 0.8274 (mmp) REVERT: A 1330 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 1350 LEU cc_start: 0.8487 (mt) cc_final: 0.8285 (mt) REVERT: A 1358 TYR cc_start: 0.8154 (m-80) cc_final: 0.7869 (m-10) REVERT: C 2 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.6766 (p0) REVERT: D 39 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: D 232 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6069 (mm-30) REVERT: E 6 GLU cc_start: 0.7852 (tp30) cc_final: 0.7413 (pt0) REVERT: E 11 LYS cc_start: 0.8205 (ttpp) cc_final: 0.6963 (mptt) REVERT: E 91 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7683 (m-40) REVERT: E 264 ASP cc_start: 0.8922 (m-30) cc_final: 0.8588 (m-30) REVERT: E 300 MET cc_start: 0.8478 (ptt) cc_final: 0.8119 (ptp) REVERT: E 315 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7505 (mtpt) REVERT: E 330 ASP cc_start: 0.7338 (m-30) cc_final: 0.6970 (m-30) REVERT: E 1000 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7927 (m110) REVERT: E 1009 LYS cc_start: 0.8149 (mttp) cc_final: 0.7802 (mtpt) REVERT: E 1018 ILE cc_start: 0.8566 (tp) cc_final: 0.8220 (tt) REVERT: E 1061 ASP cc_start: 0.7680 (p0) cc_final: 0.6911 (t0) REVERT: E 1115 TYR cc_start: 0.8759 (m-80) cc_final: 0.8473 (m-80) REVERT: E 1182 TYR cc_start: 0.8495 (m-80) cc_final: 0.8212 (m-80) REVERT: G 60 SER cc_start: 0.8659 (m) cc_final: 0.8078 (p) REVERT: H 57 LEU cc_start: 0.7389 (tp) cc_final: 0.7120 (tp) REVERT: H 224 GLN cc_start: 0.8097 (mt0) cc_final: 0.7820 (mt0) REVERT: I 6 GLU cc_start: 0.7954 (tp30) cc_final: 0.7439 (pt0) REVERT: I 11 LYS cc_start: 0.8295 (ttpp) cc_final: 0.7264 (mmtt) REVERT: I 383 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: I 906 ASN cc_start: 0.8102 (m-40) cc_final: 0.7562 (p0) REVERT: I 1009 LYS cc_start: 0.8151 (mttp) cc_final: 0.7855 (mtpt) REVERT: I 1089 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7973 (t0) REVERT: I 1157 ASP cc_start: 0.8105 (m-30) cc_final: 0.7813 (m-30) REVERT: I 1323 PHE cc_start: 0.8712 (m-80) cc_final: 0.8445 (m-80) REVERT: I 1330 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8305 (mm) REVERT: K 2 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6660 (p0) REVERT: K 9 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: L 138 LYS cc_start: 0.5539 (mptt) cc_final: 0.5260 (mttp) REVERT: L 236 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7935 (mtp180) REVERT: M 11 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7207 (mptt) REVERT: M 396 ASP cc_start: 0.8621 (m-30) cc_final: 0.8351 (m-30) REVERT: M 665 MET cc_start: 0.8800 (mmm) cc_final: 0.8303 (mmm) REVERT: M 677 ASN cc_start: 0.8809 (p0) cc_final: 0.8187 (p0) REVERT: M 979 ASP cc_start: 0.8665 (m-30) cc_final: 0.8036 (m-30) REVERT: M 1061 ASP cc_start: 0.7520 (p0) cc_final: 0.7049 (t0) REVERT: M 1241 GLN cc_start: 0.7994 (mt0) cc_final: 0.7610 (mt0) REVERT: M 1265 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7048 (mt-10) REVERT: M 1330 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8297 (mm) REVERT: M 1358 TYR cc_start: 0.8107 (m-80) cc_final: 0.7804 (m-10) REVERT: M 1364 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6186 (t0) REVERT: O 2 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6763 (p0) REVERT: P 39 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: P 124 ASP cc_start: 0.7476 (m-30) cc_final: 0.6946 (m-30) REVERT: P 232 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6087 (mm-30) REVERT: Q 6 GLU cc_start: 0.7866 (tp30) cc_final: 0.7411 (pt0) REVERT: Q 11 LYS cc_start: 0.8174 (ttpp) cc_final: 0.6923 (mptt) REVERT: Q 264 ASP cc_start: 0.8873 (m-30) cc_final: 0.8530 (m-30) REVERT: Q 315 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7626 (mtpt) REVERT: Q 341 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7136 (p0) REVERT: Q 1000 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7942 (m110) REVERT: Q 1061 ASP cc_start: 0.7786 (p0) cc_final: 0.6958 (t0) REVERT: Q 1182 TYR cc_start: 0.8487 (m-80) cc_final: 0.8222 (m-80) REVERT: T 57 LEU cc_start: 0.7497 (tp) cc_final: 0.7266 (tp) REVERT: U 6 GLU cc_start: 0.7955 (tp30) cc_final: 0.7446 (pt0) REVERT: U 11 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7106 (mmtt) REVERT: U 383 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: U 455 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8073 (tp) REVERT: U 638 GLN cc_start: 0.8325 (mt0) cc_final: 0.7890 (mt0) REVERT: U 906 ASN cc_start: 0.8081 (m-40) cc_final: 0.7389 (p0) REVERT: U 1000 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7547 (m110) REVERT: U 1009 LYS cc_start: 0.8098 (mttp) cc_final: 0.7788 (mtpt) REVERT: U 1157 ASP cc_start: 0.8105 (m-30) cc_final: 0.7833 (m-30) REVERT: U 1248 MET cc_start: 0.8499 (mmm) cc_final: 0.8187 (mmp) REVERT: U 1330 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8308 (mm) REVERT: W 9 GLU cc_start: 0.7606 (mp0) cc_final: 0.6592 (mp0) REVERT: W 236 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.5646 (mtt-85) outliers start: 174 outliers final: 125 residues processed: 1002 average time/residue: 0.8281 time to fit residues: 1451.3315 Evaluate side-chains 941 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 795 time to evaluate : 7.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 879 VAL Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1000 ASN Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1096 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 879 VAL Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1068 LEU Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1108 LEU Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 383 ASP Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 960 ASP Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1089 ASN Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1330 ILE Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 341 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 879 VAL Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 998 ASN Chi-restraints excluded: chain Q residue 1000 ASN Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1096 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 301 THR Chi-restraints excluded: chain U residue 383 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 726 ILE Chi-restraints excluded: chain U residue 879 VAL Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1044 ILE Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1068 LEU Chi-restraints excluded: chain U residue 1096 THR Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 654 optimal weight: 0.0570 chunk 422 optimal weight: 6.9990 chunk 632 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 672 optimal weight: 5.9990 chunk 721 optimal weight: 5.9990 chunk 523 optimal weight: 0.0870 chunk 98 optimal weight: 4.9990 chunk 831 optimal weight: 0.0270 overall best weight: 1.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 628 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN E 91 ASN E 141 ASN E 355 ASN E 473 ASN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN I 355 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 355 ASN M 628 ASN M 638 GLN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1089 ASN O 44 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 ASN Q 648 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1181 ASN T 224 GLN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 430 GLN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 90852 Z= 0.195 Angle : 0.484 8.867 123558 Z= 0.261 Chirality : 0.045 0.177 13626 Planarity : 0.004 0.069 16110 Dihedral : 4.482 41.730 12162 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.61 % Favored : 95.38 % Rotamer: Outliers : 1.89 % Allowed : 14.22 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.08), residues: 10974 helix: 1.18 (0.14), residues: 1590 sheet: -0.36 (0.10), residues: 2568 loop : -1.35 (0.07), residues: 6816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Q 136 HIS 0.003 0.001 HIS U 8 PHE 0.012 0.001 PHE E1277 TYR 0.016 0.001 TYR Q 197 ARG 0.006 0.000 ARG A1114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 808 time to evaluate : 7.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7262 (mptt) REVERT: A 330 ASP cc_start: 0.7082 (m-30) cc_final: 0.6559 (m-30) REVERT: A 340 LEU cc_start: 0.7292 (pt) cc_final: 0.6899 (mm) REVERT: A 650 LYS cc_start: 0.8042 (tptt) cc_final: 0.7642 (tptm) REVERT: A 665 MET cc_start: 0.8596 (mmm) cc_final: 0.8118 (mmm) REVERT: A 676 MET cc_start: 0.8396 (ppp) cc_final: 0.8140 (ptm) REVERT: A 677 ASN cc_start: 0.8836 (p0) cc_final: 0.8336 (p0) REVERT: A 1037 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: A 1149 ASN cc_start: 0.8687 (p0) cc_final: 0.8371 (p0) REVERT: A 1238 MET cc_start: 0.8285 (mmm) cc_final: 0.8023 (mmm) REVERT: A 1248 MET cc_start: 0.8578 (mmm) cc_final: 0.8116 (mmp) REVERT: A 1330 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 1358 TYR cc_start: 0.8167 (m-80) cc_final: 0.7868 (m-10) REVERT: C 2 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.6781 (p0) REVERT: D 39 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: D 232 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6109 (mm-30) REVERT: E 6 GLU cc_start: 0.7860 (tp30) cc_final: 0.7428 (pt0) REVERT: E 11 LYS cc_start: 0.8230 (ttpp) cc_final: 0.6947 (mptt) REVERT: E 91 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: E 300 MET cc_start: 0.8494 (ptt) cc_final: 0.8138 (ptp) REVERT: E 315 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7593 (mtpt) REVERT: E 330 ASP cc_start: 0.7334 (m-30) cc_final: 0.6966 (m-30) REVERT: E 1000 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8014 (m110) REVERT: E 1009 LYS cc_start: 0.8146 (mttp) cc_final: 0.7769 (mtpt) REVERT: E 1018 ILE cc_start: 0.8601 (tp) cc_final: 0.8231 (tt) REVERT: E 1061 ASP cc_start: 0.7888 (p0) cc_final: 0.6909 (t0) REVERT: E 1115 TYR cc_start: 0.8752 (m-80) cc_final: 0.8459 (m-80) REVERT: E 1182 TYR cc_start: 0.8561 (m-80) cc_final: 0.8308 (m-80) REVERT: E 1291 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7690 (mttp) REVERT: H 57 LEU cc_start: 0.7451 (tp) cc_final: 0.7160 (tp) REVERT: I 6 GLU cc_start: 0.7958 (tp30) cc_final: 0.7434 (pt0) REVERT: I 11 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7380 (mptt) REVERT: I 383 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: I 906 ASN cc_start: 0.8151 (m-40) cc_final: 0.7597 (p0) REVERT: I 1000 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7684 (m110) REVERT: I 1009 LYS cc_start: 0.8164 (mttp) cc_final: 0.7777 (mtpt) REVERT: I 1248 MET cc_start: 0.8393 (mmm) cc_final: 0.7969 (mmp) REVERT: I 1323 PHE cc_start: 0.8684 (m-80) cc_final: 0.8432 (m-80) REVERT: I 1330 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8218 (mm) REVERT: K 2 ASN cc_start: 0.7446 (OUTLIER) cc_final: 0.6811 (p0) REVERT: K 9 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: L 138 LYS cc_start: 0.5441 (mptt) cc_final: 0.5225 (mttp) REVERT: L 236 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7936 (mtp180) REVERT: M 11 LYS cc_start: 0.8112 (ttpp) cc_final: 0.7215 (mptt) REVERT: M 315 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8174 (mtpt) REVERT: M 665 MET cc_start: 0.8762 (mmm) cc_final: 0.8252 (mmm) REVERT: M 979 ASP cc_start: 0.8730 (m-30) cc_final: 0.8268 (m-30) REVERT: M 1037 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: M 1061 ASP cc_start: 0.7495 (p0) cc_final: 0.7065 (t0) REVERT: M 1238 MET cc_start: 0.8239 (mmm) cc_final: 0.7977 (mmm) REVERT: M 1330 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8305 (mm) REVERT: M 1358 TYR cc_start: 0.8125 (m-80) cc_final: 0.7813 (m-10) REVERT: M 1364 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6238 (t0) REVERT: O 2 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6749 (p0) REVERT: O 236 ARG cc_start: 0.7944 (ptp-170) cc_final: 0.5619 (mtt-85) REVERT: P 39 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: P 62 LYS cc_start: 0.6666 (ttpp) cc_final: 0.6317 (ttpp) REVERT: P 124 ASP cc_start: 0.7492 (m-30) cc_final: 0.6956 (m-30) REVERT: P 232 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6124 (mm-30) REVERT: Q 6 GLU cc_start: 0.7875 (tp30) cc_final: 0.7427 (pt0) REVERT: Q 11 LYS cc_start: 0.8188 (ttpp) cc_final: 0.6900 (mptt) REVERT: Q 315 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7663 (mtpt) REVERT: Q 341 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7142 (p0) REVERT: Q 1000 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7982 (m110) REVERT: Q 1037 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: Q 1061 ASP cc_start: 0.7835 (p0) cc_final: 0.6909 (t0) REVERT: Q 1182 TYR cc_start: 0.8545 (m-80) cc_final: 0.8291 (m-80) REVERT: T 57 LEU cc_start: 0.7615 (tp) cc_final: 0.7307 (tp) REVERT: U 6 GLU cc_start: 0.7956 (tp30) cc_final: 0.7449 (pt0) REVERT: U 11 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7325 (mmtt) REVERT: U 455 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8099 (tp) REVERT: U 638 GLN cc_start: 0.8245 (mt0) cc_final: 0.7804 (mt0) REVERT: U 984 LYS cc_start: 0.8436 (mttp) cc_final: 0.8218 (mtmt) REVERT: U 1000 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7634 (m110) REVERT: U 1009 LYS cc_start: 0.8109 (mttp) cc_final: 0.7799 (mtpt) REVERT: U 1248 MET cc_start: 0.8508 (mmm) cc_final: 0.8178 (mmp) REVERT: U 1330 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8300 (mm) REVERT: W 2 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.6942 (p0) REVERT: W 236 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.5628 (mtt-85) outliers start: 186 outliers final: 138 residues processed: 942 average time/residue: 0.8290 time to fit residues: 1358.9397 Evaluate side-chains 942 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 781 time to evaluate : 7.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 514 ASN Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 879 VAL Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1000 ASN Chi-restraints excluded: chain E residue 1026 ASN Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1089 ASN Chi-restraints excluded: chain E residue 1096 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 703 GLN Chi-restraints excluded: chain I residue 879 VAL Chi-restraints excluded: chain I residue 1000 ASN Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1108 LEU Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 960 ASP Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1017 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1037 GLU Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1330 ILE Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 192 THR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 341 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 879 VAL Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 998 ASN Chi-restraints excluded: chain Q residue 1000 ASN Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1037 GLU Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1096 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1306 THR Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain U residue 48 ASN Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 140 LEU Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 726 ILE Chi-restraints excluded: chain U residue 879 VAL Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1044 ILE Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1096 THR Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1306 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 962 optimal weight: 4.9990 chunk 1013 optimal weight: 0.9980 chunk 925 optimal weight: 3.9990 chunk 986 optimal weight: 10.0000 chunk 593 optimal weight: 0.9990 chunk 429 optimal weight: 5.9990 chunk 774 optimal weight: 4.9990 chunk 302 optimal weight: 4.9990 chunk 891 optimal weight: 9.9990 chunk 932 optimal weight: 4.9990 chunk 982 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 177 ASN A 355 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 GLN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN E 91 ASN E 141 ASN E 473 ASN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN ** E1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN I 52 ASN I 128 ASN I 177 ASN I 855 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 355 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1241 GLN O 44 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 GLN T 224 GLN U 52 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 90852 Z= 0.403 Angle : 0.587 8.405 123558 Z= 0.316 Chirality : 0.048 0.221 13626 Planarity : 0.005 0.078 16110 Dihedral : 4.912 37.499 12162 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 14.11 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.08), residues: 10974 helix: 1.03 (0.14), residues: 1578 sheet: -0.65 (0.10), residues: 2574 loop : -1.46 (0.07), residues: 6822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 136 HIS 0.005 0.001 HIS E1171 PHE 0.019 0.002 PHE E1277 TYR 0.020 0.002 TYR I1115 ARG 0.008 0.001 ARG E1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 763 time to evaluate : 7.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7287 (mptt) REVERT: A 330 ASP cc_start: 0.7124 (m-30) cc_final: 0.6635 (m-30) REVERT: A 340 LEU cc_start: 0.7801 (pt) cc_final: 0.7360 (mm) REVERT: A 676 MET cc_start: 0.8435 (ppp) cc_final: 0.7878 (ptm) REVERT: A 798 ILE cc_start: 0.8952 (mm) cc_final: 0.8745 (tp) REVERT: A 1037 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: A 1238 MET cc_start: 0.8387 (mmm) cc_final: 0.8148 (mmm) REVERT: A 1248 MET cc_start: 0.8652 (mmm) cc_final: 0.8363 (mmm) REVERT: A 1330 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 1358 TYR cc_start: 0.8204 (m-80) cc_final: 0.7942 (m-10) REVERT: C 2 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6714 (p0) REVERT: D 39 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: D 232 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6135 (mm-30) REVERT: E 6 GLU cc_start: 0.7898 (tp30) cc_final: 0.7494 (pt0) REVERT: E 11 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7027 (mptt) REVERT: E 300 MET cc_start: 0.8509 (ptt) cc_final: 0.8069 (ptp) REVERT: E 315 LYS cc_start: 0.8590 (mmmt) cc_final: 0.7757 (mtpt) REVERT: E 1000 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8279 (m110) REVERT: E 1009 LYS cc_start: 0.8151 (mttp) cc_final: 0.7792 (mtpt) REVERT: E 1018 ILE cc_start: 0.8632 (tp) cc_final: 0.8192 (tt) REVERT: E 1030 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8220 (m-40) REVERT: E 1091 ARG cc_start: 0.5606 (ptm160) cc_final: 0.5404 (ptm160) REVERT: E 1115 TYR cc_start: 0.8924 (m-80) cc_final: 0.8694 (m-80) REVERT: G 9 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7069 (mp0) REVERT: G 236 ARG cc_start: 0.8077 (ptp-170) cc_final: 0.7868 (ptp-170) REVERT: H 57 LEU cc_start: 0.7529 (tp) cc_final: 0.7112 (tp) REVERT: H 224 GLN cc_start: 0.8178 (mt0) cc_final: 0.7971 (mt0) REVERT: I 6 GLU cc_start: 0.7989 (tp30) cc_final: 0.7459 (pt0) REVERT: I 11 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7421 (mptt) REVERT: I 383 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: I 455 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8238 (tp) REVERT: I 906 ASN cc_start: 0.8226 (m-40) cc_final: 0.7630 (p0) REVERT: I 1000 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8269 (m110) REVERT: I 1009 LYS cc_start: 0.8223 (mttp) cc_final: 0.7981 (mtpt) REVERT: I 1089 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7855 (t0) REVERT: I 1293 PHE cc_start: 0.8369 (m-80) cc_final: 0.8153 (m-80) REVERT: I 1330 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (mm) REVERT: K 2 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.6936 (p0) REVERT: K 9 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: L 138 LYS cc_start: 0.5516 (mptt) cc_final: 0.5304 (mttp) REVERT: L 210 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8021 (mm-30) REVERT: M 11 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7264 (mptt) REVERT: M 195 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8041 (t0) REVERT: M 330 ASP cc_start: 0.7223 (m-30) cc_final: 0.6655 (m-30) REVERT: M 665 MET cc_start: 0.8796 (mmm) cc_final: 0.8331 (mmm) REVERT: M 959 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: M 1037 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: M 1061 ASP cc_start: 0.7574 (p0) cc_final: 0.7036 (t0) REVERT: M 1330 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8376 (mm) REVERT: M 1358 TYR cc_start: 0.8223 (m-80) cc_final: 0.7979 (m-10) REVERT: M 1364 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6575 (t0) REVERT: O 2 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.6777 (p0) REVERT: P 39 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: P 62 LYS cc_start: 0.6641 (ttpp) cc_final: 0.6308 (ttpp) REVERT: P 232 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6142 (mm-30) REVERT: Q 6 GLU cc_start: 0.7921 (tp30) cc_final: 0.7507 (pt0) REVERT: Q 11 LYS cc_start: 0.8408 (ttpp) cc_final: 0.6871 (mmtt) REVERT: Q 300 MET cc_start: 0.8575 (ptt) cc_final: 0.8266 (ptp) REVERT: Q 315 LYS cc_start: 0.8551 (mmmt) cc_final: 0.7808 (mtpt) REVERT: Q 341 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7198 (p0) REVERT: Q 1000 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8256 (m110) REVERT: Q 1030 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8195 (m-40) REVERT: Q 1037 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: Q 1061 ASP cc_start: 0.7924 (p0) cc_final: 0.6726 (t0) REVERT: Q 1089 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8045 (t0) REVERT: S 129 MET cc_start: 0.7470 (tpp) cc_final: 0.7162 (mmp) REVERT: T 57 LEU cc_start: 0.7647 (tp) cc_final: 0.7298 (tp) REVERT: U 6 GLU cc_start: 0.7990 (tp30) cc_final: 0.7472 (pt0) REVERT: U 11 LYS cc_start: 0.8419 (ttpp) cc_final: 0.7480 (mptt) REVERT: U 341 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6728 (t0) REVERT: U 383 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: U 455 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8283 (tp) REVERT: U 627 MET cc_start: 0.8976 (mtm) cc_final: 0.8735 (mtm) REVERT: U 638 GLN cc_start: 0.8253 (mt0) cc_final: 0.7879 (mt0) REVERT: U 901 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7436 (mtm180) REVERT: U 984 LYS cc_start: 0.8486 (mttp) cc_final: 0.8282 (mtmt) REVERT: U 1000 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8266 (m110) REVERT: U 1009 LYS cc_start: 0.8198 (mttp) cc_final: 0.7931 (mtpt) REVERT: U 1037 GLU cc_start: 0.7382 (tt0) cc_final: 0.7136 (tt0) REVERT: U 1089 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8085 (t0) REVERT: U 1248 MET cc_start: 0.8590 (mmm) cc_final: 0.8327 (mmp) REVERT: U 1330 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8273 (mm) REVERT: W 2 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7172 (p0) REVERT: W 9 GLU cc_start: 0.7700 (mp0) cc_final: 0.7021 (mp0) REVERT: W 236 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.5770 (mtt90) outliers start: 219 outliers final: 164 residues processed: 926 average time/residue: 0.8379 time to fit residues: 1342.5506 Evaluate side-chains 936 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 739 time to evaluate : 7.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 852 MET Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 514 ASN Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 879 VAL Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1000 ASN Chi-restraints excluded: chain E residue 1030 ASN Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1096 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1306 THR Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 177 ASN Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 514 ASN Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 703 GLN Chi-restraints excluded: chain I residue 879 VAL Chi-restraints excluded: chain I residue 1000 ASN Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 123 ILE Chi-restraints excluded: chain M residue 124 SER Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 195 ASN Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 286 LEU Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 355 ASN Chi-restraints excluded: chain M residue 383 ASP Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 663 LEU Chi-restraints excluded: chain M residue 694 ILE Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 852 MET Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 959 GLU Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1017 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1037 GLU Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1142 THR Chi-restraints excluded: chain M residue 1165 ILE Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1330 ILE Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 63 ASP Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 192 THR Chi-restraints excluded: chain Q residue 341 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 514 ASN Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 663 LEU Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 879 VAL Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 998 ASN Chi-restraints excluded: chain Q residue 1000 ASN Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1030 ASN Chi-restraints excluded: chain Q residue 1037 GLU Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1089 ASN Chi-restraints excluded: chain Q residue 1094 ILE Chi-restraints excluded: chain Q residue 1096 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1306 THR Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 128 ASN Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 169 SER Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 341 ASP Chi-restraints excluded: chain U residue 383 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 879 VAL Chi-restraints excluded: chain U residue 901 ARG Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1026 ASN Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1096 THR Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1119 THR Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1306 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 647 optimal weight: 2.9990 chunk 1042 optimal weight: 3.9990 chunk 636 optimal weight: 0.5980 chunk 494 optimal weight: 0.9990 chunk 724 optimal weight: 5.9990 chunk 1093 optimal weight: 20.0000 chunk 1006 optimal weight: 3.9990 chunk 871 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 672 optimal weight: 0.9990 chunk 534 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 355 ASN A 628 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 ASN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN G 44 ASN I 52 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 355 ASN M 628 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 998 ASN O 44 ASN ** Q 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 473 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN T 224 GLN U 52 ASN ** U 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 90852 Z= 0.158 Angle : 0.478 9.796 123558 Z= 0.258 Chirality : 0.044 0.181 13626 Planarity : 0.004 0.068 16110 Dihedral : 4.551 42.006 12162 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 1.77 % Allowed : 14.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.08), residues: 10974 helix: 1.18 (0.13), residues: 1632 sheet: -0.44 (0.10), residues: 2538 loop : -1.35 (0.07), residues: 6804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 136 HIS 0.003 0.001 HIS U 513 PHE 0.012 0.001 PHE E 242 TYR 0.013 0.001 TYR U1358 ARG 0.012 0.000 ARG Q1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21948 Ramachandran restraints generated. 10974 Oldfield, 0 Emsley, 10974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 808 time to evaluate : 8.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7284 (mptt) REVERT: A 315 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7945 (mtpt) REVERT: A 330 ASP cc_start: 0.7093 (m-30) cc_final: 0.6579 (m-30) REVERT: A 340 LEU cc_start: 0.7616 (pt) cc_final: 0.7272 (mm) REVERT: A 650 LYS cc_start: 0.8011 (tptt) cc_final: 0.7599 (tptm) REVERT: A 676 MET cc_start: 0.8388 (ppp) cc_final: 0.8111 (ptm) REVERT: A 677 ASN cc_start: 0.8805 (p0) cc_final: 0.8291 (p0) REVERT: A 1037 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 1149 ASN cc_start: 0.8664 (p0) cc_final: 0.8356 (p0) REVERT: A 1238 MET cc_start: 0.8271 (mmm) cc_final: 0.8019 (mmm) REVERT: A 1248 MET cc_start: 0.8589 (mmm) cc_final: 0.8138 (mmp) REVERT: A 1330 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8243 (mm) REVERT: A 1358 TYR cc_start: 0.8164 (m-80) cc_final: 0.7839 (m-10) REVERT: C 2 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6782 (p0) REVERT: D 39 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 232 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6119 (mm-30) REVERT: E 6 GLU cc_start: 0.7839 (tp30) cc_final: 0.7406 (pt0) REVERT: E 11 LYS cc_start: 0.8227 (ttpp) cc_final: 0.6951 (mptt) REVERT: E 264 ASP cc_start: 0.8875 (m-30) cc_final: 0.8507 (m-30) REVERT: E 300 MET cc_start: 0.8528 (ptt) cc_final: 0.8186 (ptp) REVERT: E 315 LYS cc_start: 0.8459 (mmmt) cc_final: 0.7702 (mtpt) REVERT: E 330 ASP cc_start: 0.7327 (m-30) cc_final: 0.6974 (m-30) REVERT: E 1000 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8039 (m110) REVERT: E 1009 LYS cc_start: 0.8140 (mttp) cc_final: 0.7803 (mtpt) REVERT: E 1018 ILE cc_start: 0.8584 (tp) cc_final: 0.8198 (tt) REVERT: E 1061 ASP cc_start: 0.7839 (p0) cc_final: 0.6803 (t0) REVERT: E 1115 TYR cc_start: 0.8732 (m-80) cc_final: 0.8455 (m-80) REVERT: E 1182 TYR cc_start: 0.8510 (m-80) cc_final: 0.8250 (m-80) REVERT: G 60 SER cc_start: 0.8670 (m) cc_final: 0.8104 (p) REVERT: G 129 MET cc_start: 0.7367 (tpp) cc_final: 0.7063 (mmp) REVERT: H 57 LEU cc_start: 0.7431 (tp) cc_final: 0.7228 (tp) REVERT: H 224 GLN cc_start: 0.8117 (mt0) cc_final: 0.7856 (mt0) REVERT: I 6 GLU cc_start: 0.7982 (tp30) cc_final: 0.7439 (pt0) REVERT: I 11 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7298 (mmtt) REVERT: I 340 LEU cc_start: 0.7627 (pt) cc_final: 0.7201 (mm) REVERT: I 383 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: I 455 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8231 (tp) REVERT: I 906 ASN cc_start: 0.8196 (m-40) cc_final: 0.7618 (p0) REVERT: I 1000 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7706 (m110) REVERT: I 1009 LYS cc_start: 0.8167 (mttp) cc_final: 0.7794 (mtpt) REVERT: I 1037 GLU cc_start: 0.7260 (tt0) cc_final: 0.7009 (tt0) REVERT: I 1089 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7915 (t0) REVERT: I 1323 PHE cc_start: 0.8706 (m-80) cc_final: 0.8467 (m-80) REVERT: I 1330 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8311 (mm) REVERT: K 2 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6963 (p0) REVERT: K 9 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: K 150 ASN cc_start: 0.7850 (p0) cc_final: 0.7429 (t0) REVERT: L 210 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7887 (mm-30) REVERT: L 232 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6353 (tt0) REVERT: M 11 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7240 (mptt) REVERT: M 330 ASP cc_start: 0.7156 (m-30) cc_final: 0.6600 (m-30) REVERT: M 665 MET cc_start: 0.8782 (mmm) cc_final: 0.8275 (mmm) REVERT: M 790 ILE cc_start: 0.9204 (tt) cc_final: 0.8949 (tt) REVERT: M 1037 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: M 1061 ASP cc_start: 0.7477 (p0) cc_final: 0.7072 (t0) REVERT: M 1238 MET cc_start: 0.8229 (mmm) cc_final: 0.7979 (mmm) REVERT: M 1330 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8331 (mm) REVERT: M 1358 TYR cc_start: 0.8110 (m-80) cc_final: 0.7798 (m-10) REVERT: M 1364 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6238 (t0) REVERT: O 2 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.6922 (p0) REVERT: P 39 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: P 124 ASP cc_start: 0.7438 (m-30) cc_final: 0.6842 (m-30) REVERT: P 232 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6115 (mm-30) REVERT: Q 6 GLU cc_start: 0.7857 (tp30) cc_final: 0.7480 (pt0) REVERT: Q 11 LYS cc_start: 0.8188 (ttpp) cc_final: 0.6952 (mptt) REVERT: Q 264 ASP cc_start: 0.8885 (m-30) cc_final: 0.8527 (m-30) REVERT: Q 300 MET cc_start: 0.8372 (ptt) cc_final: 0.8079 (ptt) REVERT: Q 315 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7685 (mtpt) REVERT: Q 341 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7187 (p0) REVERT: Q 1000 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8006 (m110) REVERT: Q 1030 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8195 (m-40) REVERT: Q 1061 ASP cc_start: 0.7906 (p0) cc_final: 0.6865 (t0) REVERT: Q 1182 TYR cc_start: 0.8575 (m-80) cc_final: 0.8332 (m-80) REVERT: Q 1342 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8538 (ttt180) REVERT: T 232 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6128 (tt0) REVERT: U 6 GLU cc_start: 0.7979 (tp30) cc_final: 0.7452 (pt0) REVERT: U 11 LYS cc_start: 0.8302 (ttpp) cc_final: 0.7306 (mmtt) REVERT: U 455 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8263 (tp) REVERT: U 638 GLN cc_start: 0.8329 (mt0) cc_final: 0.7901 (mt0) REVERT: U 906 ASN cc_start: 0.8094 (m-40) cc_final: 0.7380 (p0) REVERT: U 984 LYS cc_start: 0.8463 (mttp) cc_final: 0.8250 (mtmt) REVERT: U 1000 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7788 (m110) REVERT: U 1009 LYS cc_start: 0.8127 (mttp) cc_final: 0.7830 (mtpt) REVERT: U 1037 GLU cc_start: 0.7350 (tt0) cc_final: 0.7100 (tt0) REVERT: U 1089 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7736 (t0) REVERT: U 1157 ASP cc_start: 0.8100 (m-30) cc_final: 0.7849 (m-30) REVERT: U 1248 MET cc_start: 0.8552 (mmm) cc_final: 0.8259 (mmp) REVERT: U 1330 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8296 (mm) REVERT: W 2 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7025 (p0) REVERT: W 232 GLU cc_start: 0.5679 (tp30) cc_final: 0.5466 (mt-10) REVERT: W 236 ARG cc_start: 0.7617 (ptp-170) cc_final: 0.5536 (mtt-85) REVERT: X 232 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6320 (tt0) outliers start: 174 outliers final: 133 residues processed: 940 average time/residue: 0.8444 time to fit residues: 1387.5660 Evaluate side-chains 942 residues out of total 9834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 784 time to evaluate : 7.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 960 ASP Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1030 ASN Chi-restraints excluded: chain A residue 1037 GLU Chi-restraints excluded: chain A residue 1054 THR Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1119 THR Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1175 GLU Chi-restraints excluded: chain A residue 1306 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1344 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 565 VAL Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 726 ILE Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 879 VAL Chi-restraints excluded: chain E residue 887 THR Chi-restraints excluded: chain E residue 901 ARG Chi-restraints excluded: chain E residue 1000 ASN Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1044 ILE Chi-restraints excluded: chain E residue 1054 THR Chi-restraints excluded: chain E residue 1096 THR Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1119 THR Chi-restraints excluded: chain E residue 1306 THR Chi-restraints excluded: chain H residue 18 MET Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 224 THR Chi-restraints excluded: chain I residue 383 ASP Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 455 LEU Chi-restraints excluded: chain I residue 499 THR Chi-restraints excluded: chain I residue 560 VAL Chi-restraints excluded: chain I residue 703 GLN Chi-restraints excluded: chain I residue 879 VAL Chi-restraints excluded: chain I residue 1000 ASN Chi-restraints excluded: chain I residue 1014 THR Chi-restraints excluded: chain I residue 1030 ASN Chi-restraints excluded: chain I residue 1054 THR Chi-restraints excluded: chain I residue 1089 ASN Chi-restraints excluded: chain I residue 1094 ILE Chi-restraints excluded: chain I residue 1096 THR Chi-restraints excluded: chain I residue 1119 THR Chi-restraints excluded: chain I residue 1306 THR Chi-restraints excluded: chain I residue 1330 ILE Chi-restraints excluded: chain K residue 2 ASN Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain L residue 18 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 152 ASP Chi-restraints excluded: chain M residue 224 THR Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 383 ASP Chi-restraints excluded: chain M residue 414 THR Chi-restraints excluded: chain M residue 455 LEU Chi-restraints excluded: chain M residue 483 SER Chi-restraints excluded: chain M residue 560 VAL Chi-restraints excluded: chain M residue 696 SER Chi-restraints excluded: chain M residue 703 GLN Chi-restraints excluded: chain M residue 879 VAL Chi-restraints excluded: chain M residue 960 ASP Chi-restraints excluded: chain M residue 1014 THR Chi-restraints excluded: chain M residue 1017 THR Chi-restraints excluded: chain M residue 1030 ASN Chi-restraints excluded: chain M residue 1037 GLU Chi-restraints excluded: chain M residue 1054 THR Chi-restraints excluded: chain M residue 1068 LEU Chi-restraints excluded: chain M residue 1165 ILE Chi-restraints excluded: chain M residue 1175 GLU Chi-restraints excluded: chain M residue 1306 THR Chi-restraints excluded: chain M residue 1330 ILE Chi-restraints excluded: chain M residue 1344 THR Chi-restraints excluded: chain M residue 1364 ASP Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain Q residue 152 ASP Chi-restraints excluded: chain Q residue 341 ASP Chi-restraints excluded: chain Q residue 410 THR Chi-restraints excluded: chain Q residue 414 THR Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 499 THR Chi-restraints excluded: chain Q residue 565 VAL Chi-restraints excluded: chain Q residue 703 GLN Chi-restraints excluded: chain Q residue 726 ILE Chi-restraints excluded: chain Q residue 731 SER Chi-restraints excluded: chain Q residue 879 VAL Chi-restraints excluded: chain Q residue 887 THR Chi-restraints excluded: chain Q residue 901 ARG Chi-restraints excluded: chain Q residue 998 ASN Chi-restraints excluded: chain Q residue 1000 ASN Chi-restraints excluded: chain Q residue 1014 THR Chi-restraints excluded: chain Q residue 1026 ASN Chi-restraints excluded: chain Q residue 1030 ASN Chi-restraints excluded: chain Q residue 1044 ILE Chi-restraints excluded: chain Q residue 1054 THR Chi-restraints excluded: chain Q residue 1094 ILE Chi-restraints excluded: chain Q residue 1096 THR Chi-restraints excluded: chain Q residue 1108 LEU Chi-restraints excluded: chain Q residue 1119 THR Chi-restraints excluded: chain Q residue 1306 THR Chi-restraints excluded: chain T residue 18 MET Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain U residue 142 GLN Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain U residue 224 THR Chi-restraints excluded: chain U residue 264 ASP Chi-restraints excluded: chain U residue 414 THR Chi-restraints excluded: chain U residue 455 LEU Chi-restraints excluded: chain U residue 499 THR Chi-restraints excluded: chain U residue 560 VAL Chi-restraints excluded: chain U residue 703 GLN Chi-restraints excluded: chain U residue 879 VAL Chi-restraints excluded: chain U residue 1000 ASN Chi-restraints excluded: chain U residue 1014 THR Chi-restraints excluded: chain U residue 1025 ILE Chi-restraints excluded: chain U residue 1030 ASN Chi-restraints excluded: chain U residue 1054 THR Chi-restraints excluded: chain U residue 1089 ASN Chi-restraints excluded: chain U residue 1108 LEU Chi-restraints excluded: chain U residue 1295 THR Chi-restraints excluded: chain U residue 1330 ILE Chi-restraints excluded: chain W residue 2 ASN Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain X residue 18 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1098 random chunks: chunk 691 optimal weight: 9.9990 chunk 927 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 803 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 872 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 chunk 895 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 141 ASN A 177 ASN A 355 ASN A 430 GLN A 628 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 ASN C 44 ASN ** D 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN E 177 ASN E 473 ASN E 514 ASN ** E 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1089 ASN G 44 ASN I 52 ASN I 177 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 722 ASN ** I 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1089 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 177 ASN M 355 ASN M 628 ASN M 722 ASN ** M 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 44 ASN P 150 ASN Q 130 ASN Q 177 ASN Q 473 ASN Q 648 ASN ** Q 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1089 ASN ** Q1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 ASN T 224 GLN U 52 ASN U 177 ASN U 355 ASN U 430 GLN U 722 ASN ** U 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U1089 ASN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.094073 restraints weight = 110937.484| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.16 r_work: 0.2695 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 90852 Z= 0.558 Angle : 0.664 11.003 123558 Z= 0.356 Chirality : 0.051 0.207 13626 Planarity : 0.005 0.089 16110 Dihedral : 5.162 34.431 12162 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 2.44 % Allowed : 14.14 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.08), residues: 10974 helix: 0.97 (0.13), residues: 1542 sheet: -0.78 (0.10), residues: 2586 loop : -1.52 (0.07), residues: 6846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 136 HIS 0.008 0.002 HIS E 834 PHE 0.023 0.003 PHE E1277 TYR 0.028 0.002 TYR I1115 ARG 0.009 0.001 ARG E 981 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22011.07 seconds wall clock time: 397 minutes 5.62 seconds (23825.62 seconds total)