Starting phenix.real_space_refine on Tue Feb 20 08:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtx_32804/02_2024/7wtx_32804.pdb" } resolution = 3.1 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= 0.011 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1604 5.49 5 S 234 5.16 5 C 47552 2.51 5 N 15521 2.21 5 O 20161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 85074 Number of models: 1 Model: "" Number of chains: 36 Chain: "2" Number of atoms: 34277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1605, 34277 Inner-chain residues flagged as termini: ['pdbres=" C 21698 "'] Classifications: {'RNA': 1605} Modifications used: {'5*END': 1, 'rna2p_pur': 126, 'rna2p_pyr': 101, 'rna3p_pur': 727, 'rna3p_pyr': 651} Link IDs: {'rna2p': 226, 'rna3p': 1378} Chain breaks: 15 Chain: "F" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "R" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 911 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1083 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "c" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 498 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain breaks: 1 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 438 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "x" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1391 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "y" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2568 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 5062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5062 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "w" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2248 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 15, 'TRANS': 259} Chain breaks: 1 Chain: "t" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1131 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 3 Chain: "K" Number of atoms: 7302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7302 Classifications: {'peptide': 940} Link IDs: {'CIS': 1, 'PTRANS': 43, 'TRANS': 895} Chain breaks: 6 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43304 SG CYS f 145 191.065 144.446 41.996 1.00 27.95 S ATOM 68214 SG CYS y 270 110.755 166.357 152.220 1.00 8.08 S ATOM 68234 SG CYS y 273 113.701 166.346 154.162 1.00 7.51 S ATOM 68331 SG CYS y 285 114.424 167.744 150.932 1.00 8.56 S ATOM 68353 SG CYS y 288 113.550 164.078 150.987 1.00 7.45 S Time building chain proxies: 33.16, per 1000 atoms: 0.39 Number of scatterers: 85074 At special positions: 0 Unit cell: (239.334, 249.924, 201.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 234 16.00 P 1604 15.00 O 20161 8.00 N 15521 7.00 C 47552 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: 30.75 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 200 " pdb="ZN ZN f 200 " - pdb=" SG CYS f 145 " pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " Number of angles added : 6 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11958 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 49 sheets defined 46.5% alpha, 14.1% beta 514 base pairs and 876 stacking pairs defined. Time for finding SS restraints: 25.64 Creating SS restraints... Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.604A pdb=" N GLY F 21 " --> pdb=" O LYS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 77 Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 162 removed outlier: 3.588A pdb=" N ALA F 162 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 204 Processing helix chain 'M' and resid 13 through 28 removed outlier: 5.296A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 44 removed outlier: 3.520A pdb=" N ALA M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU M 42 " --> pdb=" O ALA M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 72 removed outlier: 4.177A pdb=" N HIS M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 119 through 132 Processing helix chain 'P' and resid 21 through 27 Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.898A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.704A pdb=" N MET P 111 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 108 through 112' Processing helix chain 'P' and resid 116 through 120 Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 52 removed outlier: 3.635A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 Processing helix chain 'Q' and resid 60 through 64 Processing helix chain 'Q' and resid 77 through 99 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.629A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 21 Processing helix chain 'R' and resid 27 through 39 Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.607A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 83 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 25 through 32 Processing helix chain 'S' and resid 37 through 47 Processing helix chain 'S' and resid 60 through 73 removed outlier: 3.666A pdb=" N VAL S 64 " --> pdb=" O THR S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.597A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.711A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 11 through 26 removed outlier: 3.508A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.813A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.692A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.561A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.542A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 144 removed outlier: 3.641A pdb=" N LYS T 144 " --> pdb=" O ALA T 140 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 removed outlier: 3.730A pdb=" N LEU Z 77 " --> pdb=" O VAL Z 73 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'f' and resid 100 through 104 removed outlier: 3.909A pdb=" N LEU f 103 " --> pdb=" O LEU f 100 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS f 104 " --> pdb=" O ALA f 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 100 through 104' Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.520A pdb=" N VAL A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.603A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLN A 36 " --> pdb=" O GLN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.619A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.755A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.733A pdb=" N PHE A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.842A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.684A pdb=" N GLY B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 62' Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.567A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 177 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 Processing helix chain 'B' and resid 224 through 233 removed outlier: 4.038A pdb=" N LEU B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.249A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.391A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 160 Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 232 through 250 removed outlier: 4.578A pdb=" N TYR C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.688A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.907A pdb=" N LYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.882A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.625A pdb=" N GLN E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 262 Processing helix chain 'G' and resid 20 through 28 removed outlier: 3.668A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 153 through 157 removed outlier: 4.139A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.600A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 37 through 43 removed outlier: 3.580A pdb=" N ARG H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 4.218A pdb=" N LYS H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.643A pdb=" N VAL H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.700A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.569A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 155 removed outlier: 3.988A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 191 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 62 removed outlier: 4.161A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 96 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.965A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 152 through 155 removed outlier: 3.878A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 155' Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.933A pdb=" N GLY N 59 " --> pdb=" O ARG N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.701A pdb=" N LYS N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 61 Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 109 through 122 removed outlier: 3.648A pdb=" N GLN O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 63 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.571A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.612A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.648A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 24 through 32 Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 93 Processing helix chain 'Y' and resid 103 through 116 removed outlier: 3.545A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 4.066A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.522A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 43 removed outlier: 3.611A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 81 through 83 No H-bonds generated for 'chain 'x' and resid 81 through 83' Processing helix chain 'x' and resid 84 through 91 Processing helix chain 'x' and resid 91 through 102 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 129 through 143 Processing helix chain 'x' and resid 145 through 155 removed outlier: 3.992A pdb=" N LEU x 152 " --> pdb=" O ASP x 148 " (cutoff:3.500A) Processing helix chain 'x' and resid 166 through 168 No H-bonds generated for 'chain 'x' and resid 166 through 168' Processing helix chain 'x' and resid 173 through 185 Processing helix chain 'x' and resid 188 through 199 Processing helix chain 'x' and resid 214 through 229 Processing helix chain 'x' and resid 233 through 248 Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.686A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) Processing helix chain 'y' and resid 30 through 36 removed outlier: 3.779A pdb=" N VAL y 34 " --> pdb=" O ILE y 30 " (cutoff:3.500A) Processing helix chain 'y' and resid 39 through 47 Processing helix chain 'y' and resid 59 through 71 removed outlier: 3.772A pdb=" N VAL y 63 " --> pdb=" O LEU y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 99 through 103 removed outlier: 3.845A pdb=" N HIS y 102 " --> pdb=" O GLY y 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU y 103 " --> pdb=" O VAL y 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 99 through 103' Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.787A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'u' and resid 49 through 72 Processing helix chain 'u' and resid 95 through 104 removed outlier: 3.861A pdb=" N ALA u 99 " --> pdb=" O SER u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 142 through 151 Processing helix chain 'u' and resid 167 through 181 Processing helix chain 'u' and resid 196 through 212 removed outlier: 3.756A pdb=" N ASP u 202 " --> pdb=" O LYS u 198 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU u 212 " --> pdb=" O SER u 208 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 removed outlier: 3.504A pdb=" N ASN u 238 " --> pdb=" O ARG u 234 " (cutoff:3.500A) Processing helix chain 'u' and resid 244 through 250 removed outlier: 3.868A pdb=" N ARG u 250 " --> pdb=" O PHE u 246 " (cutoff:3.500A) Processing helix chain 'u' and resid 398 through 403 Processing helix chain 'u' and resid 465 through 484 removed outlier: 3.555A pdb=" N GLU u 482 " --> pdb=" O GLU u 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET u 483 " --> pdb=" O ARG u 479 " (cutoff:3.500A) Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 523 through 526 Processing helix chain 'u' and resid 532 through 546 Processing helix chain 'u' and resid 567 through 576 removed outlier: 3.973A pdb=" N GLU u 571 " --> pdb=" O VAL u 567 " (cutoff:3.500A) Processing helix chain 'u' and resid 719 through 726 removed outlier: 4.142A pdb=" N VAL u 723 " --> pdb=" O ASN u 719 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 72 Processing helix chain 'w' and resid 180 through 193 Processing helix chain 'w' and resid 206 through 210 Processing helix chain 'w' and resid 212 through 220 removed outlier: 3.669A pdb=" N ILE w 216 " --> pdb=" O ASN w 212 " (cutoff:3.500A) Processing helix chain 'w' and resid 221 through 225 Processing helix chain 'w' and resid 226 through 240 Processing helix chain 'w' and resid 242 through 253 Processing helix chain 'w' and resid 253 through 266 removed outlier: 3.511A pdb=" N ALA w 263 " --> pdb=" O ARG w 259 " (cutoff:3.500A) Processing helix chain 'w' and resid 269 through 280 Processing helix chain 'w' and resid 282 through 290 Processing helix chain 'w' and resid 290 through 298 removed outlier: 4.028A pdb=" N GLY w 298 " --> pdb=" O LEU w 294 " (cutoff:3.500A) Processing helix chain 'w' and resid 301 through 315 removed outlier: 3.616A pdb=" N CYS w 315 " --> pdb=" O ILE w 311 " (cutoff:3.500A) Processing helix chain 'w' and resid 318 through 332 removed outlier: 3.530A pdb=" N MET w 332 " --> pdb=" O LYS w 328 " (cutoff:3.500A) Processing helix chain 'w' and resid 337 through 347 removed outlier: 3.644A pdb=" N PHE w 341 " --> pdb=" O ALA w 337 " (cutoff:3.500A) Processing helix chain 'w' and resid 353 through 367 Processing helix chain 'w' and resid 375 through 389 removed outlier: 3.776A pdb=" N HIS w 379 " --> pdb=" O PRO w 375 " (cutoff:3.500A) Processing helix chain 'w' and resid 394 through 408 Processing helix chain 'w' and resid 412 through 423 removed outlier: 4.094A pdb=" N GLU w 416 " --> pdb=" O GLN w 412 " (cutoff:3.500A) Processing helix chain 't' and resid 292 through 307 Processing helix chain 't' and resid 351 through 357 removed outlier: 3.591A pdb=" N TYR t 357 " --> pdb=" O CYS t 354 " (cutoff:3.500A) Processing helix chain 't' and resid 426 through 469 Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 117 through 122 removed outlier: 3.672A pdb=" N LYS K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 removed outlier: 3.650A pdb=" N GLU K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 141 removed outlier: 3.642A pdb=" N LYS K 141 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 151 through 156 Processing helix chain 'K' and resid 162 through 175 removed outlier: 4.036A pdb=" N VAL K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 Processing helix chain 'K' and resid 186 through 205 Processing helix chain 'K' and resid 207 through 224 Processing helix chain 'K' and resid 233 through 243 Processing helix chain 'K' and resid 249 through 265 Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 302 through 315 removed outlier: 3.909A pdb=" N HIS K 306 " --> pdb=" O THR K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 335 Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.690A pdb=" N ALA K 355 " --> pdb=" O SER K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 375 removed outlier: 3.550A pdb=" N TYR K 375 " --> pdb=" O ILE K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 405 removed outlier: 4.015A pdb=" N ALA K 389 " --> pdb=" O GLN K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 424 Proline residue: K 414 - end of helix Processing helix chain 'K' and resid 428 through 447 removed outlier: 3.526A pdb=" N LEU K 432 " --> pdb=" O HIS K 428 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 455 Processing helix chain 'K' and resid 463 through 478 Processing helix chain 'K' and resid 486 through 506 removed outlier: 6.766A pdb=" N ARG K 503 " --> pdb=" O GLU K 499 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN K 504 " --> pdb=" O ALA K 500 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 520 Processing helix chain 'K' and resid 527 through 543 Processing helix chain 'K' and resid 543 through 551 removed outlier: 3.570A pdb=" N VAL K 547 " --> pdb=" O GLY K 543 " (cutoff:3.500A) Processing helix chain 'K' and resid 568 through 577 Processing helix chain 'K' and resid 581 through 606 removed outlier: 4.023A pdb=" N PHE K 585 " --> pdb=" O ARG K 581 " (cutoff:3.500A) Proline residue: K 591 - end of helix Processing helix chain 'K' and resid 608 through 624 removed outlier: 3.841A pdb=" N SER K 612 " --> pdb=" O SER K 608 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS K 613 " --> pdb=" O THR K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 630 Processing helix chain 'K' and resid 635 through 640 removed outlier: 3.571A pdb=" N PHE K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) Processing helix chain 'K' and resid 643 through 653 Processing helix chain 'K' and resid 654 through 673 removed outlier: 3.613A pdb=" N ARG K 658 " --> pdb=" O ARG K 654 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL K 659 " --> pdb=" O PRO K 655 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR K 660 " --> pdb=" O ASP K 656 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS K 673 " --> pdb=" O ILE K 669 " (cutoff:3.500A) Processing helix chain 'K' and resid 675 through 698 removed outlier: 3.834A pdb=" N ARG K 679 " --> pdb=" O ALA K 675 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN K 688 " --> pdb=" O ARG K 684 " (cutoff:3.500A) Proline residue: K 691 - end of helix Processing helix chain 'K' and resid 709 through 723 removed outlier: 3.523A pdb=" N VAL K 713 " --> pdb=" O PRO K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 725 through 742 Processing helix chain 'K' and resid 746 through 761 Processing helix chain 'K' and resid 762 through 764 No H-bonds generated for 'chain 'K' and resid 762 through 764' Processing helix chain 'K' and resid 765 through 777 Processing helix chain 'K' and resid 778 through 782 removed outlier: 3.670A pdb=" N GLU K 781 " --> pdb=" O PRO K 778 " (cutoff:3.500A) Processing helix chain 'K' and resid 784 through 801 removed outlier: 4.003A pdb=" N SER K 801 " --> pdb=" O GLU K 797 " (cutoff:3.500A) Processing helix chain 'K' and resid 804 through 813 Processing helix chain 'K' and resid 813 through 824 Processing helix chain 'K' and resid 832 through 843 removed outlier: 4.025A pdb=" N LYS K 838 " --> pdb=" O ARG K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 851 through 867 removed outlier: 3.548A pdb=" N ILE K 855 " --> pdb=" O HIS K 851 " (cutoff:3.500A) Proline residue: K 860 - end of helix Processing helix chain 'K' and resid 870 through 888 Processing helix chain 'K' and resid 894 through 905 Processing helix chain 'K' and resid 906 through 911 Processing helix chain 'K' and resid 913 through 931 removed outlier: 3.606A pdb=" N PHE K 929 " --> pdb=" O THR K 925 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU K 930 " --> pdb=" O HIS K 926 " (cutoff:3.500A) Processing helix chain 'K' and resid 936 through 951 Processing helix chain 'K' and resid 955 through 973 Processing helix chain 'K' and resid 974 through 979 Processing helix chain 'K' and resid 981 through 991 removed outlier: 3.533A pdb=" N VAL K 985 " --> pdb=" O HIS K 981 " (cutoff:3.500A) Processing helix chain 'K' and resid 994 through 1000 Processing helix chain 'K' and resid 1000 through 1015 Processing helix chain 'K' and resid 1016 through 1024 removed outlier: 3.564A pdb=" N VAL K1020 " --> pdb=" O GLY K1016 " (cutoff:3.500A) Processing helix chain 'K' and resid 1025 through 1042 removed outlier: 3.651A pdb=" N HIS K1029 " --> pdb=" O PRO K1025 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG K1030 " --> pdb=" O GLU K1026 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL K1031 " --> pdb=" O GLU K1027 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA K1040 " --> pdb=" O ARG K1036 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K1041 " --> pdb=" O LYS K1037 " (cutoff:3.500A) Processing helix chain 'K' and resid 1122 through 1127 removed outlier: 4.514A pdb=" N ALA K1126 " --> pdb=" O PRO K1123 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 123 through 127 removed outlier: 18.064A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 13.112A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS c 27 " --> pdb=" O GLY c 19 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY c 19 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 31 through 34 Processing sheet with id=AA3, first strand: chain 'P' and resid 76 through 78 removed outlier: 5.876A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR P 97 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR P 78 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 10 through 16 Processing sheet with id=AA5, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'T' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AA9, first strand: chain 'Z' and resid 67 through 68 removed outlier: 6.249A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AB2, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.663A pdb=" N LYS A 40 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.795A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.520A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.520A pdb=" N THR B 98 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.249A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.147A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 102 through 116 removed outlier: 6.631A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 115 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY C 119 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 137 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.330A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.689A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 128 through 132 Processing sheet with id=AC3, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.145A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.987A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN G 56 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU G 109 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY G 54 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU G 111 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE G 52 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE G 113 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 50 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS G 115 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR G 48 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR G 48 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'H' and resid 47 through 52 removed outlier: 4.402A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.338A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.323A pdb=" N LYS I 37 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.205A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AD3, first strand: chain 'L' and resid 72 through 79 removed outlier: 16.679A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.703A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 52 through 55 removed outlier: 7.572A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 32 through 39 removed outlier: 4.915A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AD7, first strand: chain 'W' and resid 80 through 81 Processing sheet with id=AD8, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.404A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id=AE1, first strand: chain 'Y' and resid 6 through 9 removed outlier: 7.573A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AE3, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.806A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'x' and resid 75 through 79 removed outlier: 8.562A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AE6, first strand: chain 'y' and resid 28 through 29 Processing sheet with id=AE7, first strand: chain 'y' and resid 111 through 112 removed outlier: 6.481A pdb=" N LYS y 111 " --> pdb=" O MET y 308 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 110 through 113 Processing sheet with id=AE9, first strand: chain 'u' and resid 251 through 254 Processing sheet with id=AF1, first strand: chain 'u' and resid 257 through 264 removed outlier: 7.476A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY u 270 " --> pdb=" O GLU u 564 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU u 564 " --> pdb=" O GLY u 270 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N SER u 563 " --> pdb=" O MET u 299 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N MET u 299 " --> pdb=" O SER u 563 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA u 304 " --> pdb=" O LEU u 344 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU u 344 " --> pdb=" O ALA u 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'u' and resid 528 through 530 Processing sheet with id=AF3, first strand: chain 'u' and resid 623 through 625 removed outlier: 6.508A pdb=" N LYS u 669 " --> pdb=" O LEU u 678 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU u 678 " --> pdb=" O LYS u 669 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE u 629 " --> pdb=" O GLN u 641 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS u 639 " --> pdb=" O GLN u 631 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU u 640 " --> pdb=" O ARG u 696 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N VAL u 698 " --> pdb=" O LEU u 640 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU u 743 " --> pdb=" O LYS u 752 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET u 710 " --> pdb=" O PHE u 707 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG u 714 " --> pdb=" O PRO u 703 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 1108 through 1109 2352 hydrogen bonds defined for protein. 6720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1274 hydrogen bonds 1984 hydrogen bond angles 0 basepair planarities 514 basepair parallelities 876 stacking parallelities Total time for adding SS restraints: 67.48 Time building geometry restraints manager: 33.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 10348 1.30 - 1.43: 32873 1.43 - 1.56: 43242 1.56 - 1.69: 3195 1.69 - 1.82: 361 Bond restraints: 90019 Sorted by residual: bond pdb=" C GLY I 30 " pdb=" N ARG I 31 " ideal model delta sigma weight residual 1.326 1.245 0.081 1.12e-02 7.97e+03 5.19e+01 bond pdb=" C VAL O 132 " pdb=" N THR O 133 " ideal model delta sigma weight residual 1.333 1.253 0.079 1.59e-02 3.96e+03 2.50e+01 bond pdb=" O3' U 21323 " pdb=" P G 21324 " ideal model delta sigma weight residual 1.607 1.539 0.068 1.50e-02 4.44e+03 2.05e+01 bond pdb=" C TYR K 907 " pdb=" N PRO K 908 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.19e-02 7.06e+03 1.40e+01 bond pdb=" C6 A 21196 " pdb=" N1 A 21196 " ideal model delta sigma weight residual 1.351 1.282 0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 90014 not shown) Histogram of bond angle deviations from ideal: 92.26 - 102.58: 2640 102.58 - 112.89: 56645 112.89 - 123.20: 59668 123.20 - 133.52: 10166 133.52 - 143.83: 91 Bond angle restraints: 129210 Sorted by residual: angle pdb=" O2' G 21324 " pdb=" C2' G 21324 " pdb=" C1' G 21324 " ideal model delta sigma weight residual 111.80 92.26 19.54 1.50e+00 4.44e-01 1.70e+02 angle pdb=" C4' U 21492 " pdb=" C3' U 21492 " pdb=" O3' U 21492 " ideal model delta sigma weight residual 113.00 97.84 15.16 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C4' G 21324 " pdb=" C3' G 21324 " pdb=" O3' G 21324 " ideal model delta sigma weight residual 109.40 98.43 10.97 1.50e+00 4.44e-01 5.34e+01 angle pdb=" O3' G 21322 " pdb=" C3' G 21322 " pdb=" C2' G 21322 " ideal model delta sigma weight residual 109.50 120.26 -10.76 1.50e+00 4.44e-01 5.15e+01 angle pdb=" N GLY F 80 " pdb=" CA GLY F 80 " pdb=" C GLY F 80 " ideal model delta sigma weight residual 112.50 120.63 -8.13 1.16e+00 7.43e-01 4.91e+01 ... (remaining 129205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 52064 35.81 - 71.62: 4426 71.62 - 107.43: 519 107.43 - 143.24: 15 143.24 - 179.05: 28 Dihedral angle restraints: 57052 sinusoidal: 38605 harmonic: 18447 Sorted by residual: dihedral pdb=" CA VAL K 378 " pdb=" C VAL K 378 " pdb=" N PRO K 379 " pdb=" CA PRO K 379 " ideal model delta harmonic sigma weight residual 180.00 -132.97 -47.03 0 5.00e+00 4.00e-02 8.85e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual 200.00 20.95 179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual -160.00 18.14 -178.14 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 57049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 14332 0.090 - 0.180: 1347 0.180 - 0.270: 111 0.270 - 0.360: 25 0.360 - 0.450: 8 Chirality restraints: 15823 Sorted by residual: chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CB ILE I 3 " pdb=" CA ILE I 3 " pdb=" CG1 ILE I 3 " pdb=" CG2 ILE I 3 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CB VAL B 210 " pdb=" CA VAL B 210 " pdb=" CG1 VAL B 210 " pdb=" CG2 VAL B 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 15820 not shown) Planarity restraints: 10433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 2 509 " -0.048 2.00e-02 2.50e+03 4.15e-02 5.16e+01 pdb=" N9 G 2 509 " 0.016 2.00e-02 2.50e+03 pdb=" C8 G 2 509 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 2 509 " 0.009 2.00e-02 2.50e+03 pdb=" C5 G 2 509 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G 2 509 " 0.075 2.00e-02 2.50e+03 pdb=" O6 G 2 509 " -0.067 2.00e-02 2.50e+03 pdb=" N1 G 2 509 " -0.049 2.00e-02 2.50e+03 pdb=" C2 G 2 509 " 0.069 2.00e-02 2.50e+03 pdb=" N2 G 2 509 " -0.021 2.00e-02 2.50e+03 pdb=" N3 G 2 509 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G 2 509 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21221 " 0.041 2.00e-02 2.50e+03 3.89e-02 4.55e+01 pdb=" N9 G 21221 " -0.019 2.00e-02 2.50e+03 pdb=" C8 G 21221 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G 21221 " -0.008 2.00e-02 2.50e+03 pdb=" C5 G 21221 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G 21221 " -0.091 2.00e-02 2.50e+03 pdb=" O6 G 21221 " 0.087 2.00e-02 2.50e+03 pdb=" N1 G 21221 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 21221 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 21221 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 21221 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 21221 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 2 492 " 0.005 2.00e-02 2.50e+03 4.16e-02 3.89e+01 pdb=" N1 C 2 492 " -0.011 2.00e-02 2.50e+03 pdb=" C2 C 2 492 " -0.097 2.00e-02 2.50e+03 pdb=" O2 C 2 492 " 0.071 2.00e-02 2.50e+03 pdb=" N3 C 2 492 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C 2 492 " -0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 492 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C 2 492 " 0.018 2.00e-02 2.50e+03 pdb=" C6 C 2 492 " 0.017 2.00e-02 2.50e+03 ... (remaining 10430 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 7564 2.73 - 3.27: 74890 3.27 - 3.81: 160980 3.81 - 4.36: 197495 4.36 - 4.90: 289743 Nonbonded interactions: 730672 Sorted by model distance: nonbonded pdb=" O2' U 2 918 " pdb=" O4' A 2 919 " model vdw 2.184 2.440 nonbonded pdb=" OH TYR E 54 " pdb=" OE2 GLU E 97 " model vdw 2.186 2.440 nonbonded pdb=" OG1 THR b 67 " pdb=" O LYS b 70 " model vdw 2.203 2.440 nonbonded pdb=" OP2 C 21153 " pdb=" NZ LYS W 71 " model vdw 2.204 2.520 nonbonded pdb=" N4 C 2 492 " pdb=" OP2 G 2 507 " model vdw 2.211 2.520 ... (remaining 730667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.790 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: 0.090 Extract box with map and model: 13.090 Check model and map are aligned: 0.920 Set scattering table: 0.590 Process input model: 233.980 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 256.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 90019 Z= 0.483 Angle : 1.035 22.420 129210 Z= 0.535 Chirality : 0.055 0.450 15823 Planarity : 0.009 0.237 10433 Dihedral : 21.934 179.049 45094 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 0.04 % Allowed : 0.60 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.05 % 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: -1.33 (0.10), residues: 6269 helix: -0.37 (0.09), residues: 2646 sheet: -0.53 (0.17), residues: 821 loop : -1.42 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP w 286 HIS 0.018 0.002 HIS P 79 PHE 0.042 0.003 PHE C 236 TYR 0.040 0.003 TYR B 205 ARG 0.017 0.001 ARG G 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 700 time to evaluate : 5.347 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: O 122 SER cc_start: 0.8042 (p) cc_final: 0.7711 (p) REVERT: O 124 MET cc_start: 0.7997 (mmt) cc_final: 0.7757 (mmt) REVERT: X 61 GLN cc_start: 0.5623 (tp-100) cc_final: 0.5255 (tp40) REVERT: u 149 MET cc_start: 0.8085 (ptt) cc_final: 0.7858 (ptt) outliers start: 2 outliers final: 0 residues processed: 702 average time/residue: 0.8329 time to fit residues: 983.5440 Evaluate side-chains 599 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 599 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 662 optimal weight: 0.9990 chunk 594 optimal weight: 1.9990 chunk 330 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 chunk 401 optimal weight: 0.9980 chunk 317 optimal weight: 0.9980 chunk 615 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 457 optimal weight: 7.9990 chunk 712 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 GLN Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN I 88 ASN I 116 HIS I 138 ASN N 62 GLN O 26 ASN V 21 ASN W 15 ASN Y 22 GLN u 631 GLN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 842 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 90019 Z= 0.171 Angle : 0.607 11.972 129210 Z= 0.312 Chirality : 0.038 0.311 15823 Planarity : 0.005 0.065 10433 Dihedral : 23.010 179.799 32068 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 0.85 % Allowed : 6.98 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 6269 helix: 0.66 (0.10), residues: 2691 sheet: -0.44 (0.17), residues: 845 loop : -1.17 (0.11), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP w 286 HIS 0.010 0.001 HIS K 977 PHE 0.046 0.002 PHE y 69 TYR 0.028 0.001 TYR K 720 ARG 0.012 0.000 ARG K 520 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 660 time to evaluate : 5.490 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: F 76 MET cc_start: 0.7300 (tpp) cc_final: 0.6888 (tpp) REVERT: R 83 ASN cc_start: 0.7271 (t0) cc_final: 0.7022 (t0) REVERT: f 89 LYS cc_start: 0.4220 (OUTLIER) cc_final: 0.3991 (ptmt) REVERT: B 217 MET cc_start: 0.7884 (mmm) cc_final: 0.7407 (mmt) REVERT: C 205 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8384 (t) REVERT: O 122 SER cc_start: 0.8047 (p) cc_final: 0.7710 (p) REVERT: u 596 MET cc_start: 0.8635 (mtm) cc_final: 0.8386 (mtt) REVERT: w 280 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6358 (tp) outliers start: 47 outliers final: 26 residues processed: 680 average time/residue: 0.8248 time to fit residues: 948.6842 Evaluate side-chains 619 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 590 time to evaluate : 5.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain f residue 89 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 77 ASP Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 282 ARG Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain K residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 396 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 593 optimal weight: 0.0270 chunk 485 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 714 optimal weight: 20.0000 chunk 771 optimal weight: 50.0000 chunk 636 optimal weight: 7.9990 chunk 708 optimal weight: 40.0000 chunk 243 optimal weight: 3.9990 chunk 572 optimal weight: 10.0000 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 83 ASN P 79 HIS Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 115 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN N 58 HIS V 21 ASN W 15 ASN Y 85 ASN y 102 HIS y 402 ASN u 239 GLN ** u 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 90019 Z= 0.422 Angle : 0.754 12.078 129210 Z= 0.379 Chirality : 0.045 0.416 15823 Planarity : 0.006 0.092 10433 Dihedral : 23.000 179.773 32068 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 1.98 % Allowed : 10.87 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 6269 helix: 0.91 (0.10), residues: 2695 sheet: -0.43 (0.17), residues: 828 loop : -1.19 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP w 213 HIS 0.014 0.002 HIS P 79 PHE 0.046 0.002 PHE J 147 TYR 0.028 0.002 TYR I 27 ARG 0.012 0.001 ARG c 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 608 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7755 (mmm) cc_final: 0.7292 (mmp) REVERT: E 12 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8202 (p) REVERT: E 148 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8178 (ptp-170) REVERT: E 199 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: L 118 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6871 (tpp-160) REVERT: O 122 SER cc_start: 0.8169 (p) cc_final: 0.7825 (p) REVERT: b 72 ARG cc_start: 0.7579 (ptm-80) cc_final: 0.7275 (ptm-80) REVERT: b 83 GLN cc_start: 0.6346 (pp30) cc_final: 0.6045 (pp30) REVERT: x 160 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8013 (pp) REVERT: u 100 MET cc_start: 0.7331 (mmm) cc_final: 0.6980 (mmm) REVERT: u 180 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: u 596 MET cc_start: 0.8697 (mtm) cc_final: 0.8439 (mtt) REVERT: w 280 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6571 (tp) REVERT: K 509 MET cc_start: 0.3043 (mtp) cc_final: 0.2788 (mtm) outliers start: 109 outliers final: 62 residues processed: 680 average time/residue: 0.8333 time to fit residues: 957.6107 Evaluate side-chains 648 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 580 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 282 ARG Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 259 ASP Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 719 ASN Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 191 VAL Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain K residue 394 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 705 optimal weight: 40.0000 chunk 536 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 479 optimal weight: 0.9990 chunk 716 optimal weight: 30.0000 chunk 758 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 679 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN V 21 ASN u 477 GLN u 740 HIS ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 730 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 90019 Z= 0.298 Angle : 0.654 10.868 129210 Z= 0.332 Chirality : 0.041 0.357 15823 Planarity : 0.005 0.063 10433 Dihedral : 22.880 178.800 32068 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.09 % Allowed : 13.34 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 6269 helix: 1.15 (0.10), residues: 2690 sheet: -0.44 (0.17), residues: 820 loop : -1.13 (0.11), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP w 213 HIS 0.008 0.001 HIS I 22 PHE 0.032 0.002 PHE J 147 TYR 0.023 0.002 TYR K 720 ARG 0.008 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 606 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 217 MET cc_start: 0.7731 (mmm) cc_final: 0.7270 (mmt) REVERT: C 152 ARG cc_start: 0.7060 (ptp-170) cc_final: 0.6747 (mtm110) REVERT: E 148 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8147 (ptp-170) REVERT: O 122 SER cc_start: 0.8167 (p) cc_final: 0.7877 (p) REVERT: O 149 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6721 (tpp-160) REVERT: X 36 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6976 (tp) REVERT: b 72 ARG cc_start: 0.7532 (ptm-80) cc_final: 0.7215 (ptm-80) REVERT: u 128 ARG cc_start: 0.7485 (ttt90) cc_final: 0.6983 (ttp-170) REVERT: u 180 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: u 596 MET cc_start: 0.8703 (mtm) cc_final: 0.8380 (mtm) REVERT: w 280 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6620 (tp) outliers start: 115 outliers final: 74 residues processed: 685 average time/residue: 0.8558 time to fit residues: 997.4743 Evaluate side-chains 662 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 582 time to evaluate : 5.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 36 LEU Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 282 ARG Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 326 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 719 ASN Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain K residue 117 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 631 optimal weight: 6.9990 chunk 430 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 564 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 647 optimal weight: 5.9990 chunk 524 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 387 optimal weight: 6.9990 chunk 681 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS H 168 HIS N 62 GLN N 90 HIS V 21 ASN ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 740 HIS ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 90019 Z= 0.281 Angle : 0.644 9.958 129210 Z= 0.327 Chirality : 0.040 0.358 15823 Planarity : 0.005 0.063 10433 Dihedral : 22.819 179.148 32068 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.34 % Allowed : 14.66 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 6269 helix: 1.29 (0.10), residues: 2699 sheet: -0.38 (0.17), residues: 826 loop : -1.12 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP w 213 HIS 0.007 0.001 HIS I 22 PHE 0.032 0.002 PHE J 147 TYR 0.021 0.002 TYR K 720 ARG 0.006 0.000 ARG L 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 605 time to evaluate : 7.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 217 MET cc_start: 0.7662 (mmm) cc_final: 0.7145 (mmt) REVERT: C 152 ARG cc_start: 0.7087 (ptp-170) cc_final: 0.6859 (mtm110) REVERT: E 19 MET cc_start: 0.8570 (mtm) cc_final: 0.8284 (mtm) REVERT: E 148 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (ptp-170) REVERT: I 56 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7443 (tpp-160) REVERT: O 122 SER cc_start: 0.8165 (p) cc_final: 0.7868 (p) REVERT: O 149 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6623 (tpp-160) REVERT: b 72 ARG cc_start: 0.7413 (ptm-80) cc_final: 0.7074 (ptm-80) REVERT: x 158 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8391 (mp) REVERT: x 160 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7940 (pp) REVERT: u 128 ARG cc_start: 0.7504 (ttt90) cc_final: 0.7054 (ttp-170) REVERT: u 180 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: u 596 MET cc_start: 0.8738 (mtm) cc_final: 0.8407 (mtm) REVERT: w 280 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6850 (tp) outliers start: 129 outliers final: 89 residues processed: 693 average time/residue: 0.8383 time to fit residues: 983.2778 Evaluate side-chains 680 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 583 time to evaluate : 5.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 282 ARG Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 326 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 259 ASP Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 719 ASN Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain t residue 419 SER Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 720 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 255 optimal weight: 8.9990 chunk 683 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 445 optimal weight: 4.9990 chunk 187 optimal weight: 50.0000 chunk 759 optimal weight: 50.0000 chunk 630 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 398 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 86 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN A 131 HIS B 40 ASN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN V 21 ASN X 39 ASN x 102 HIS x 110 ASN u 256 HIS u 740 HIS ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 338 ASN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 506 HIS K1133 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 90019 Z= 0.481 Angle : 0.798 12.399 129210 Z= 0.398 Chirality : 0.048 0.428 15823 Planarity : 0.007 0.098 10433 Dihedral : 22.936 179.933 32068 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 2.87 % Allowed : 15.76 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.10), residues: 6269 helix: 1.16 (0.10), residues: 2689 sheet: -0.44 (0.17), residues: 835 loop : -1.19 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP w 213 HIS 0.011 0.001 HIS I 22 PHE 0.046 0.002 PHE J 147 TYR 0.025 0.002 TYR A 139 ARG 0.011 0.001 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 591 time to evaluate : 5.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 CYS cc_start: 0.5194 (t) cc_final: 0.4947 (t) REVERT: A 145 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8615 (mt) REVERT: B 217 MET cc_start: 0.7813 (mmm) cc_final: 0.7317 (mmt) REVERT: C 183 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7370 (pttt) REVERT: E 19 MET cc_start: 0.8632 (mtm) cc_final: 0.8416 (mtm) REVERT: E 148 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7467 (ptp-170) REVERT: I 56 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7799 (tpp-160) REVERT: J 154 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: J 159 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.6629 (t80) REVERT: O 84 ARG cc_start: 0.7451 (tpt90) cc_final: 0.7114 (tpt90) REVERT: O 122 SER cc_start: 0.8221 (p) cc_final: 0.7924 (p) REVERT: O 149 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6798 (tpp-160) REVERT: b 6 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.6226 (p0) REVERT: b 72 ARG cc_start: 0.7441 (ptm-80) cc_final: 0.7095 (ptm-80) REVERT: x 158 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8443 (mp) REVERT: x 160 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8061 (pp) REVERT: u 128 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7081 (ttp-170) REVERT: u 180 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: u 596 MET cc_start: 0.8755 (mtm) cc_final: 0.8470 (mtm) REVERT: u 743 GLU cc_start: 0.6611 (tt0) cc_final: 0.5932 (tt0) REVERT: w 280 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6982 (tp) REVERT: K 542 MET cc_start: 0.3090 (tpt) cc_final: 0.2691 (tpt) outliers start: 158 outliers final: 109 residues processed: 707 average time/residue: 0.8652 time to fit residues: 1037.2204 Evaluate side-chains 694 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 573 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 104 ASP Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 234 CYS Chi-restraints excluded: chain y residue 253 LEU Chi-restraints excluded: chain y residue 282 ARG Chi-restraints excluded: chain y residue 326 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 163 LEU Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 259 ASP Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 654 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 719 ASN Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 191 VAL Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 338 ASN Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain t residue 419 SER Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 720 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 732 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 432 optimal weight: 2.9990 chunk 554 optimal weight: 1.9990 chunk 429 optimal weight: 0.4980 chunk 639 optimal weight: 3.9990 chunk 424 optimal weight: 0.8980 chunk 756 optimal weight: 40.0000 chunk 473 optimal weight: 3.9990 chunk 461 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN F 179 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN x 110 ASN ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 90019 Z= 0.209 Angle : 0.606 12.575 129210 Z= 0.309 Chirality : 0.038 0.322 15823 Planarity : 0.004 0.057 10433 Dihedral : 22.751 178.061 32068 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 2.18 % Allowed : 16.74 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 6269 helix: 1.45 (0.10), residues: 2687 sheet: -0.47 (0.17), residues: 832 loop : -1.04 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP w 213 HIS 0.007 0.001 HIS K 506 PHE 0.032 0.001 PHE T 14 TYR 0.021 0.001 TYR K 720 ARG 0.010 0.000 ARG f 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 612 time to evaluate : 5.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 217 MET cc_start: 0.7710 (mmm) cc_final: 0.7490 (mmt) REVERT: E 19 MET cc_start: 0.8573 (mtm) cc_final: 0.8352 (mtm) REVERT: E 148 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8081 (ptp-170) REVERT: H 145 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7033 (tpp-160) REVERT: I 5 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6582 (ptm-80) REVERT: J 154 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: J 159 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6679 (t80) REVERT: O 122 SER cc_start: 0.8245 (p) cc_final: 0.7960 (p) REVERT: O 149 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6711 (tpp-160) REVERT: b 6 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6149 (p0) REVERT: b 72 ARG cc_start: 0.7401 (ptm-80) cc_final: 0.7034 (ptm-80) REVERT: x 158 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8401 (mp) REVERT: x 160 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8053 (pp) REVERT: u 61 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7710 (mtm-85) REVERT: u 128 ARG cc_start: 0.7559 (ttt90) cc_final: 0.7081 (ttp-170) REVERT: u 596 MET cc_start: 0.8728 (mtm) cc_final: 0.8416 (mtm) REVERT: u 721 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: w 280 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7002 (tp) REVERT: w 367 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6903 (m-80) outliers start: 120 outliers final: 76 residues processed: 695 average time/residue: 0.8315 time to fit residues: 980.2257 Evaluate side-chains 681 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 591 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain f residue 148 TYR Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 91 THR Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 326 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 645 THR Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 721 GLU Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 367 PHE Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 720 TYR Chi-restraints excluded: chain K residue 725 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 468 optimal weight: 0.0070 chunk 302 optimal weight: 5.9990 chunk 451 optimal weight: 0.0570 chunk 227 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 30.0000 chunk 481 optimal weight: 5.9990 chunk 515 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 chunk 70 optimal weight: 50.0000 chunk 594 optimal weight: 3.9990 overall best weight: 2.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 137 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN V 21 ASN x 110 ASN ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 90019 Z= 0.250 Angle : 0.629 11.390 129210 Z= 0.319 Chirality : 0.039 0.348 15823 Planarity : 0.005 0.064 10433 Dihedral : 22.694 178.882 32068 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 2.20 % Allowed : 16.94 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 6269 helix: 1.47 (0.10), residues: 2689 sheet: -0.45 (0.17), residues: 821 loop : -0.99 (0.12), residues: 2759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP w 213 HIS 0.007 0.001 HIS x 210 PHE 0.030 0.002 PHE J 147 TYR 0.021 0.001 TYR K 720 ARG 0.013 0.000 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 596 time to evaluate : 5.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 CYS cc_start: 0.5185 (t) cc_final: 0.4936 (t) REVERT: A 118 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: A 136 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6831 (mt-10) REVERT: A 145 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8618 (mt) REVERT: C 183 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7111 (ptmt) REVERT: E 19 MET cc_start: 0.8601 (mtm) cc_final: 0.8388 (mtm) REVERT: E 148 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8093 (ptp-170) REVERT: I 5 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.6584 (ptm-80) REVERT: I 56 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7446 (tpp-160) REVERT: J 154 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: J 159 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6708 (t80) REVERT: O 122 SER cc_start: 0.8278 (p) cc_final: 0.7987 (p) REVERT: O 149 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6699 (tpp-160) REVERT: b 6 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6223 (p0) REVERT: b 72 ARG cc_start: 0.7386 (ptm-80) cc_final: 0.7017 (ptm-80) REVERT: x 158 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (mp) REVERT: x 160 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8059 (pp) REVERT: u 61 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7776 (mtm-85) REVERT: u 128 ARG cc_start: 0.7549 (ttt90) cc_final: 0.7089 (ttp-170) REVERT: u 180 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: u 596 MET cc_start: 0.8731 (mtm) cc_final: 0.8400 (mtm) REVERT: u 721 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: w 280 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6992 (tp) REVERT: w 367 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6915 (m-80) outliers start: 121 outliers final: 83 residues processed: 686 average time/residue: 0.8202 time to fit residues: 949.8782 Evaluate side-chains 682 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 581 time to evaluate : 5.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 721 GLU Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 367 PHE Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain t residue 419 SER Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 720 TYR Chi-restraints excluded: chain K residue 725 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 688 optimal weight: 5.9990 chunk 724 optimal weight: 50.0000 chunk 661 optimal weight: 3.9990 chunk 705 optimal weight: 5.9990 chunk 424 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 553 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 637 optimal weight: 0.9980 chunk 666 optimal weight: 5.9990 chunk 702 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN x 110 ASN ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 90019 Z= 0.261 Angle : 0.635 11.799 129210 Z= 0.322 Chirality : 0.040 0.344 15823 Planarity : 0.005 0.082 10433 Dihedral : 22.670 178.836 32068 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 2.36 % Allowed : 16.83 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 6269 helix: 1.49 (0.10), residues: 2688 sheet: -0.47 (0.17), residues: 823 loop : -1.00 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP w 213 HIS 0.007 0.001 HIS x 210 PHE 0.030 0.002 PHE J 147 TYR 0.021 0.002 TYR K 720 ARG 0.010 0.000 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 594 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 131 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6931 (mp) REVERT: A 118 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: A 136 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: A 145 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8624 (mt) REVERT: C 183 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7052 (ptmt) REVERT: E 148 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8022 (ptp-170) REVERT: I 5 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6617 (ptm-80) REVERT: I 56 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7460 (tpp-160) REVERT: J 154 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: J 159 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6660 (t80) REVERT: L 139 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8099 (mmt-90) REVERT: O 122 SER cc_start: 0.8229 (p) cc_final: 0.7949 (p) REVERT: O 149 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6676 (tpp-160) REVERT: b 6 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.6167 (p0) REVERT: x 158 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8395 (mp) REVERT: x 160 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8064 (pp) REVERT: u 61 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7736 (mtm-85) REVERT: u 128 ARG cc_start: 0.7576 (ttt90) cc_final: 0.7097 (ttp-170) REVERT: u 596 MET cc_start: 0.8731 (mtm) cc_final: 0.8391 (mtm) REVERT: u 743 GLU cc_start: 0.6443 (tt0) cc_final: 0.5903 (tt0) REVERT: w 280 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6928 (tp) REVERT: w 367 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: K 155 MET cc_start: 0.1699 (pmm) cc_final: 0.1402 (pmm) outliers start: 130 outliers final: 96 residues processed: 688 average time/residue: 0.8252 time to fit residues: 958.9219 Evaluate side-chains 699 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 585 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain c residue 45 ASN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 139 ARG Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain e residue 29 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 88 LEU Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 207 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 259 ASP Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 217 LEU Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 367 PHE Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain t residue 419 SER Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 720 TYR Chi-restraints excluded: chain K residue 725 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 462 optimal weight: 0.3980 chunk 745 optimal weight: 50.0000 chunk 455 optimal weight: 10.0000 chunk 353 optimal weight: 0.9980 chunk 518 optimal weight: 0.8980 chunk 782 optimal weight: 5.9990 chunk 719 optimal weight: 9.9990 chunk 622 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 481 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN ** u 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 321 HIS ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 90019 Z= 0.193 Angle : 0.607 14.988 129210 Z= 0.308 Chirality : 0.038 0.321 15823 Planarity : 0.004 0.087 10433 Dihedral : 22.647 178.408 32068 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 1.98 % Allowed : 17.25 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.11), residues: 6269 helix: 1.54 (0.10), residues: 2692 sheet: -0.48 (0.17), residues: 830 loop : -0.94 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP w 213 HIS 0.006 0.001 HIS x 210 PHE 0.024 0.001 PHE J 147 TYR 0.021 0.001 TYR K 720 ARG 0.010 0.000 ARG G 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12538 Ramachandran restraints generated. 6269 Oldfield, 0 Emsley, 6269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 597 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: A 136 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: A 145 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8617 (mt) REVERT: C 183 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7001 (ptmt) REVERT: C 232 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7628 (m) REVERT: E 148 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7994 (ptp-170) REVERT: I 5 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.6559 (ptm-80) REVERT: I 56 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7454 (tpp-160) REVERT: J 154 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: J 159 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.6586 (t80) REVERT: O 122 SER cc_start: 0.8226 (p) cc_final: 0.7944 (p) REVERT: O 149 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6689 (tpp-160) REVERT: b 6 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6138 (p0) REVERT: x 158 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (mp) REVERT: x 160 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8056 (pp) REVERT: u 61 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7594 (mtm-85) REVERT: u 128 ARG cc_start: 0.7543 (ttt90) cc_final: 0.7010 (ttp-170) REVERT: u 596 MET cc_start: 0.8715 (mtm) cc_final: 0.8366 (mtm) REVERT: u 743 GLU cc_start: 0.6351 (tt0) cc_final: 0.5766 (tt0) REVERT: w 280 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6891 (tp) REVERT: w 367 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: K 155 MET cc_start: 0.1745 (pmm) cc_final: 0.1340 (pmm) outliers start: 109 outliers final: 84 residues processed: 676 average time/residue: 0.8299 time to fit residues: 952.1829 Evaluate side-chains 689 residues out of total 5517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 588 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 44 VAL Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 90 SER Chi-restraints excluded: chain c residue 28 THR Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain I residue 56 ARG Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 138 ASN Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 159 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain N residue 87 ASP Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 135 ILE Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 32 ILE Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 26 ASP Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain Y residue 47 MET Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain x residue 80 VAL Chi-restraints excluded: chain x residue 158 LEU Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 229 ILE Chi-restraints excluded: chain x residue 250 ASP Chi-restraints excluded: chain y residue 53 LEU Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain u residue 61 ARG Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 79 ASP Chi-restraints excluded: chain u residue 180 GLN Chi-restraints excluded: chain u residue 182 LEU Chi-restraints excluded: chain u residue 217 HIS Chi-restraints excluded: chain u residue 222 LEU Chi-restraints excluded: chain u residue 261 VAL Chi-restraints excluded: chain u residue 297 PHE Chi-restraints excluded: chain u residue 486 ASP Chi-restraints excluded: chain u residue 565 VAL Chi-restraints excluded: chain u residue 658 ILE Chi-restraints excluded: chain u residue 687 VAL Chi-restraints excluded: chain u residue 766 LEU Chi-restraints excluded: chain u residue 778 THR Chi-restraints excluded: chain w residue 280 LEU Chi-restraints excluded: chain w residue 367 PHE Chi-restraints excluded: chain w residue 395 THR Chi-restraints excluded: chain w residue 425 VAL Chi-restraints excluded: chain t residue 350 CYS Chi-restraints excluded: chain t residue 419 SER Chi-restraints excluded: chain K residue 117 ASN Chi-restraints excluded: chain K residue 457 VAL Chi-restraints excluded: chain K residue 720 TYR Chi-restraints excluded: chain K residue 725 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 785 random chunks: chunk 494 optimal weight: 4.9990 chunk 663 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 574 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 623 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 640 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 GLN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN V 21 ASN x 110 ASN ** w 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 321 HIS w 338 ASN ** w 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 842 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.144390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128708 restraints weight = 141135.573| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.25 r_work: 0.3523 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 90019 Z= 0.478 Angle : 0.796 15.224 129210 Z= 0.395 Chirality : 0.047 0.427 15823 Planarity : 0.006 0.098 10433 Dihedral : 22.804 179.989 32068 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.63 % Favored : 95.33 % Rotamer: Outliers : 2.36 % Allowed : 17.06 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.02 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 6269 helix: 1.32 (0.10), residues: 2685 sheet: -0.52 (0.17), residues: 842 loop : -1.10 (0.11), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP w 213 HIS 0.013 0.001 HIS C 136 PHE 0.046 0.002 PHE J 147 TYR 0.024 0.002 TYR A 139 ARG 0.009 0.001 ARG G 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16673.20 seconds wall clock time: 296 minutes 27.67 seconds (17787.67 seconds total)