Starting phenix.real_space_refine on Sun Jan 26 10:43:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.map" model { file = "/net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zxe_11518/01_2025/6zxe_11518.cif" } resolution = 3.0 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1038 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1645 5.49 5 S 190 5.16 5 C 44268 2.51 5 N 14836 2.21 5 O 19559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 80500 Number of models: 1 Model: "" Number of chains: 39 Chain: "2" Number of atoms: 35125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1645, 35125 Classifications: {'RNA': 1645} Modifications used: {'rna2p_pur': 128, 'rna2p_pyr': 107, 'rna3p_pur': 744, 'rna3p_pyr': 666} Link IDs: {'rna2p': 235, 'rna3p': 1409} Chain breaks: 13 Chain: "R" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 990 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 375 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain breaks: 1 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: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2246 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 186 Chain: "d" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52} Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} 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: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} 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: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1151 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} 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: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "Z" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "f" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 478 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "g" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2439 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 303} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "k" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2886 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 36, 'TRANS': 393} Chain breaks: 5 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 432 Unresolved non-hydrogen angles: 545 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 187 Chain: "z" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1317 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 240} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 889 Unresolved non-hydrogen angles: 1110 Unresolved non-hydrogen dihedrals: 749 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 479 Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" 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 60613 SG CYS y 270 114.074 162.220 149.817 1.00 5.51 S ATOM 60633 SG CYS y 273 116.944 162.033 152.302 1.00 4.71 S ATOM 60730 SG CYS y 285 118.182 163.119 148.886 1.00 5.83 S ATOM 60752 SG CYS y 288 116.959 159.803 149.318 1.00 4.95 S Time building chain proxies: 33.41, per 1000 atoms: 0.42 Number of scatterers: 80500 At special positions: 0 Unit cell: (220.272, 243.57, 199.092, 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 190 16.00 P 1645 15.00 O 19559 8.00 N 14836 7.00 C 44268 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.53 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " Number of angles added : 6 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10970 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 63 sheets defined 34.4% alpha, 16.1% beta 468 base pairs and 899 stacking pairs defined. Time for finding SS restraints: 26.08 Creating SS restraints... Processing helix chain 'R' and resid 6 through 19 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.660A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 61 removed outlier: 3.616A pdb=" N LYS R 49 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'R' and resid 74 through 83 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'A' and resid 11 through 22 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: 3.778A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.951A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.609A pdb=" N ALA A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 removed outlier: 3.883A pdb=" N SER B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 57 through 61 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 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 removed outlier: 3.881A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.826A 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 78 through 83 Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.205A pdb=" N ILE C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 161 removed outlier: 3.983A pdb=" N SER C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.510A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (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 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 247 through 262 removed outlier: 3.754A pdb=" N SER E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 39 through 42 removed outlier: 4.010A pdb=" N GLY G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 39 through 42' Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.508A pdb=" N PHE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 removed outlier: 3.702A pdb=" N GLN G 155 " --> pdb=" O ASP G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 229 Processing helix chain 'H' and resid 17 through 34 removed outlier: 3.719A pdb=" N SER H 21 " --> pdb=" O ASP H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 42 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 75 removed outlier: 3.664A pdb=" N PHE H 72 " --> pdb=" O GLN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 87 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 117 through 120 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.638A pdb=" N VAL H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.990A 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 88 through 93 removed outlier: 4.029A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 93' Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 131 through 136 removed outlier: 3.605A pdb=" N ILE I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 153 removed outlier: 3.636A pdb=" N GLN I 146 " --> pdb=" O SER I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 156 No H-bonds generated for 'chain 'I' and resid 154 through 156' 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 204 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 39 through 61 removed outlier: 4.153A 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 95 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.941A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 116 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.582A pdb=" N ALA J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.808A pdb=" N GLN J 154 " --> pdb=" O LEU J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 179 Processing helix chain 'L' and resid 23 through 30 removed outlier: 4.303A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 52 removed outlier: 3.514A pdb=" N ILE L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 42 Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.830A 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 Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 70 through 86 Processing helix chain 'O' and resid 109 through 122 Processing helix chain 'V' and resid 56 through 62 removed outlier: 3.656A pdb=" N ARG V 60 " --> pdb=" O CYS V 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.674A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 43 Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 33 removed outlier: 3.579A pdb=" N LYS X 28 " --> pdb=" O ASP X 24 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 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 removed outlier: 3.515A pdb=" N GLU Y 86 " --> pdb=" O ALA Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 93 removed outlier: 3.685A pdb=" N ARG Y 93 " --> pdb=" O HIS Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 115 Processing helix chain 'Y' and resid 119 through 125 removed outlier: 3.766A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 17 Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 43 removed outlier: 3.772A pdb=" N ARG e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL e 43 " --> pdb=" O ASN e 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 81 through 84 Processing helix chain 'x' and resid 85 through 91 Processing helix chain 'x' and resid 92 through 101 Proline residue: x 98 - end of helix Processing helix chain 'x' and resid 129 through 143 removed outlier: 3.560A pdb=" N GLY x 143 " --> pdb=" O ALA x 139 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 150 Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.636A pdb=" N ARG x 154 " --> pdb=" O LEU x 150 " (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 230 Processing helix chain 'x' and resid 233 through 247 removed outlier: 3.744A pdb=" N VAL x 237 " --> pdb=" O PRO x 233 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG x 247 " --> pdb=" O ALA x 243 " (cutoff:3.500A) Processing helix chain 'y' and resid 10 through 16 removed outlier: 3.983A pdb=" N PHE y 14 " --> pdb=" O ASP y 10 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG y 16 " --> pdb=" O GLY y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 36 removed outlier: 3.656A pdb=" N THR y 35 " --> pdb=" O ARG y 31 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 31 through 36' Processing helix chain 'y' and resid 39 through 47 removed outlier: 3.658A pdb=" N ALA y 47 " --> pdb=" O ARG y 43 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 71 removed outlier: 3.646A pdb=" N VAL y 63 " --> pdb=" O LEU y 59 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) Processing helix chain 'y' and resid 80 through 98 Processing helix chain 'y' and resid 238 through 249 Processing helix chain 'y' and resid 363 through 367 removed outlier: 4.318A pdb=" N ILE y 367 " --> pdb=" O PRO y 364 " (cutoff:3.500A) Processing helix chain 'y' and resid 380 through 385 removed outlier: 3.743A pdb=" N THR y 384 " --> pdb=" O SER y 380 " (cutoff:3.500A) Processing helix chain 'y' and resid 393 through 398 removed outlier: 3.543A pdb=" N ARG y 397 " --> pdb=" O GLY y 393 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 19 removed outlier: 3.597A pdb=" N ARG d 19 " --> pdb=" O GLN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 3.738A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR d 46 " --> pdb=" O CYS d 42 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 removed outlier: 3.719A pdb=" N GLY D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 63 through 77 removed outlier: 3.888A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 removed outlier: 4.147A pdb=" N GLU D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 105 " --> pdb=" O GLN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 removed outlier: 4.048A pdb=" N GLY D 121 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 123 " --> pdb=" O CYS D 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'F' and resid 18 through 22 Processing helix chain 'F' and resid 33 through 38 removed outlier: 3.550A pdb=" N GLN F 36 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 76 removed outlier: 3.800A pdb=" N ARG F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.628A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 104 removed outlier: 4.578A pdb=" N GLU F 98 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.749A pdb=" N VAL F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 3.540A pdb=" N ARG F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.585A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.735A pdb=" N LYS F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.755A pdb=" N ALA K 10 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE K 16 " --> pdb=" O TYR K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 54 removed outlier: 3.942A pdb=" N SER K 54 " --> pdb=" O GLN K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 83 removed outlier: 4.613A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU K 79 " --> pdb=" O GLY K 75 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG K 80 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 65 through 70 removed outlier: 4.281A pdb=" N ALA M 70 " --> pdb=" O GLU M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 90 removed outlier: 3.886A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 130 removed outlier: 3.611A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 37 removed outlier: 3.667A pdb=" N LEU P 36 " --> pdb=" O LEU P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 52 through 58 removed outlier: 3.753A pdb=" N LEU P 56 " --> pdb=" O LYS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 66 removed outlier: 3.526A pdb=" N LYS P 65 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 61 through 66' Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.552A pdb=" N MET P 89 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 86 through 90' Processing helix chain 'P' and resid 108 through 112 Processing helix chain 'P' and resid 116 through 120 Processing helix chain 'Q' and resid 38 through 42 removed outlier: 3.636A pdb=" N ILE Q 42 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 48 Processing helix chain 'Q' and resid 51 through 59 removed outlier: 4.361A pdb=" N VAL Q 55 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU Q 57 " --> pdb=" O GLU Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.589A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 82 Processing helix chain 'Q' and resid 83 through 99 removed outlier: 3.883A pdb=" N ILE Q 88 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 91 " --> pdb=" O SER Q 87 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU Q 92 " --> pdb=" O ILE Q 88 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL Q 93 " --> pdb=" O SER Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.671A pdb=" N GLU Q 107 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE Q 108 " --> pdb=" O SER Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'S' and resid 29 through 33 removed outlier: 3.883A pdb=" N ILE S 33 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 47 Processing helix chain 'S' and resid 63 through 73 removed outlier: 4.063A pdb=" N VAL S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.750A pdb=" N TYR S 77 " --> pdb=" O PRO S 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 74 through 78' Processing helix chain 'S' and resid 99 through 104 Processing helix chain 'S' and resid 107 through 116 removed outlier: 4.003A pdb=" N LEU S 111 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU S 112 " --> pdb=" O ARG S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 removed outlier: 4.568A pdb=" N LEU S 123 " --> pdb=" O ALA S 119 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG S 124 " --> pdb=" O HIS S 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.691A pdb=" N ASP T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 9' Processing helix chain 'T' and resid 10 through 26 removed outlier: 3.510A pdb=" N ALA T 19 " --> pdb=" O VAL T 15 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER T 25 " --> pdb=" O PHE T 21 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.785A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.533A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR T 65 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 removed outlier: 3.799A pdb=" N THR T 76 " --> pdb=" O VAL T 72 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR T 79 " --> pdb=" O MET T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 105 Processing helix chain 'T' and resid 124 through 138 removed outlier: 4.082A pdb=" N ASP T 130 " --> pdb=" O GLN T 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 46 removed outlier: 3.608A pdb=" N GLY U 42 " --> pdb=" O ASP U 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA U 43 " --> pdb=" O LEU U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 101 removed outlier: 3.749A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 104 No H-bonds generated for 'chain 'U' and resid 102 through 104' Processing helix chain 'Z' and resid 51 through 60 removed outlier: 4.324A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 65 Processing helix chain 'Z' and resid 71 through 76 Processing helix chain 'Z' and resid 82 through 95 removed outlier: 3.714A pdb=" N ALA Z 86 " --> pdb=" O SER Z 82 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU Z 91 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 105 Processing helix chain 'k' and resid 11 through 19 Processing helix chain 'k' and resid 31 through 36 removed outlier: 3.757A pdb=" N VAL k 35 " --> pdb=" O LEU k 31 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG k 36 " --> pdb=" O GLU k 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 31 through 36' Processing helix chain 'k' and resid 43 through 48 removed outlier: 3.619A pdb=" N LEU k 46 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 74 removed outlier: 3.665A pdb=" N GLY k 73 " --> pdb=" O GLY k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 147 through 152 Processing helix chain 'k' and resid 195 through 201 removed outlier: 4.388A pdb=" N ALA k 199 " --> pdb=" O PRO k 196 " (cutoff:3.500A) Processing helix chain 'k' and resid 220 through 224 Processing helix chain 'k' and resid 241 through 247 removed outlier: 3.663A pdb=" N SER k 247 " --> pdb=" O GLU k 243 " (cutoff:3.500A) Processing helix chain 'k' and resid 250 through 260 removed outlier: 3.658A pdb=" N VAL k 260 " --> pdb=" O GLU k 256 " (cutoff:3.500A) Processing helix chain 'k' and resid 351 through 366 removed outlier: 4.270A pdb=" N GLN k 359 " --> pdb=" O PHE k 355 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR k 360 " --> pdb=" O LEU k 356 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU k 364 " --> pdb=" O THR k 360 " (cutoff:3.500A) Processing helix chain 'k' and resid 393 through 397 removed outlier: 3.836A pdb=" N ASP k 396 " --> pdb=" O PRO k 393 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU k 397 " --> pdb=" O PRO k 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 393 through 397' Processing helix chain 'k' and resid 415 through 420 removed outlier: 3.788A pdb=" N GLU k 419 " --> pdb=" O GLN k 415 " (cutoff:3.500A) Processing helix chain 'k' and resid 490 through 502 removed outlier: 3.645A pdb=" N ASP k 494 " --> pdb=" O GLN k 490 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU k 499 " --> pdb=" O VAL k 495 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE k 500 " --> pdb=" O MET k 496 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU k 501 " --> pdb=" O ASP k 497 " (cutoff:3.500A) Processing helix chain 'z' and resid 164 through 177 removed outlier: 3.665A pdb=" N ILE z 169 " --> pdb=" O ARG z 165 " (cutoff:3.500A) Processing helix chain 'z' and resid 241 through 258 Processing helix chain 'z' and resid 300 through 319 removed outlier: 4.312A pdb=" N LEU z 305 " --> pdb=" O ARG z 301 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN z 306 " --> pdb=" O GLU z 302 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP z 317 " --> pdb=" O ARG z 313 " (cutoff:3.500A) Processing helix chain 'z' and resid 352 through 371 removed outlier: 3.848A pdb=" N LEU z 357 " --> pdb=" O ALA z 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS z 359 " --> pdb=" O GLU z 355 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA z 362 " --> pdb=" O ARG z 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL z 364 " --> pdb=" O ASP z 360 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE z 367 " --> pdb=" O ASN z 363 " (cutoff:3.500A) Processing helix chain 'z' and resid 377 through 386 Processing helix chain 'z' and resid 395 through 408 removed outlier: 3.565A pdb=" N ALA z 402 " --> pdb=" O TYR z 398 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 421 removed outlier: 3.688A pdb=" N GLN z 417 " --> pdb=" O GLU z 413 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP z 418 " --> pdb=" O ARG z 414 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL z 420 " --> pdb=" O SER z 416 " (cutoff:3.500A) Processing helix chain 'z' and resid 422 through 426 removed outlier: 3.562A pdb=" N LYS z 426 " --> pdb=" O GLU z 423 " (cutoff:3.500A) Processing helix chain 'z' and resid 532 through 544 removed outlier: 3.661A pdb=" N MET z 537 " --> pdb=" O GLU z 533 " (cutoff:3.500A) Processing helix chain 'z' and resid 551 through 559 removed outlier: 3.594A pdb=" N GLU z 559 " --> pdb=" O LYS z 555 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.988A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.415A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 75 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.916A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 50 removed outlier: 3.916A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 98 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS B 34 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N PHE B 100 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 13.924A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.026A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL B 212 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 116 removed outlier: 5.539A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 184 through 187 Processing sheet with id=AA8, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA9, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.542A pdb=" N ILE E 90 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.509A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 217 through 219 removed outlier: 3.657A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS E 230 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.665A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 53 removed outlier: 7.729A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 185 through 188 removed outlier: 6.025A pdb=" N LEU H 153 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE H 144 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS H 155 " --> pdb=" O LYS H 142 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS H 142 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS H 157 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.337A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.301A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 62 through 67 removed outlier: 5.605A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS I 100 " --> pdb=" O ILE I 175 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 136 through 137 removed outlier: 3.582A pdb=" N GLN J 140 " --> pdb=" O VAL J 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.609A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.666A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.419A pdb=" N VAL O 27 " --> pdb=" O ILE O 90 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR O 91 " --> pdb=" O LYS O 125 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLY O 127 " --> pdb=" O THR O 91 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 15 through 16 removed outlier: 4.653A pdb=" N ARG V 15 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.326A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC8, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.649A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 56 through 58 removed outlier: 6.627A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 56 through 58 removed outlier: 4.194A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id=AD3, first strand: chain 'Y' and resid 6 through 9 removed outlier: 7.616A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 32 through 34 Processing sheet with id=AD5, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.634A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'x' and resid 75 through 79 removed outlier: 3.504A pdb=" N ASN x 115 " --> pdb=" O ASN x 110 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS y 129 " --> pdb=" O ILE x 107 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE x 109 " --> pdb=" O HIS y 129 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'x' and resid 159 through 164 Processing sheet with id=AD8, first strand: chain 'y' and resid 114 through 115 removed outlier: 3.624A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER y 311 " --> pdb=" O LYS y 295 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N LYS y 295 " --> pdb=" O SER y 311 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain 'D' and resid 34 through 38 removed outlier: 6.597A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU D 89 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 150 through 155 removed outlier: 3.872A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 183 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 225 through 226 removed outlier: 6.974A pdb=" N VAL g 176 " --> pdb=" O LYS g 185 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN g 187 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL g 174 " --> pdb=" O ASN g 187 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS g 175 " --> pdb=" O SER g 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER g 167 " --> pdb=" O LYS g 175 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 123 through 124 Processing sheet with id=AE5, first strand: chain 'K' and resid 21 through 22 removed outlier: 3.644A pdb=" N HIS K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA K 63 " --> pdb=" O HIS K 66 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 31 through 33 removed outlier: 4.206A pdb=" N VAL M 109 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL M 51 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.213A pdb=" N VAL P 76 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR P 97 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR P 78 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL P 94 " --> pdb=" O VAL P 105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 15 removed outlier: 3.990A pdb=" N THR Q 20 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS Q 73 " --> pdb=" O THR Q 20 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 81 through 83 removed outlier: 3.652A pdb=" N SER T 93 " --> pdb=" O GLY T 81 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AF2, first strand: chain 'U' and resid 49 through 50 removed outlier: 4.401A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE U 84 " --> pdb=" O THR U 58 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR U 58 " --> pdb=" O ILE U 84 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS U 86 " --> pdb=" O MET U 56 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 49 through 50 removed outlier: 4.401A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER U 26 " --> pdb=" O HIS U 85 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 63 through 66 Processing sheet with id=AF5, first strand: chain 'Z' and resid 98 through 101 removed outlier: 5.640A pdb=" N LEU Z 99 " --> pdb=" O THR Z 110 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N THR Z 110 " --> pdb=" O LEU Z 99 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 43 through 46 removed outlier: 8.544A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR c 15 " --> pdb=" O ARG c 31 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU c 33 " --> pdb=" O ARG c 13 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS c 10 " --> pdb=" O LEU c 58 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 133 through 134 Processing sheet with id=AF8, first strand: chain 'g' and resid 5 through 12 removed outlier: 6.239A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 21 through 23 removed outlier: 4.292A pdb=" N ILE g 31 " --> pdb=" O TRP g 43 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP g 43 " --> pdb=" O ILE g 31 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER g 33 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE g 41 " --> pdb=" O SER g 33 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.603A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 108 through 112 removed outlier: 7.361A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE g 129 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR g 141 " --> pdb=" O ILE g 129 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU g 131 " --> pdb=" O LYS g 139 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 199 through 200 removed outlier: 4.672A pdb=" N CYS g 207 " --> pdb=" O TRP g 219 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP g 219 " --> pdb=" O CYS g 207 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 239 through 241 removed outlier: 3.927A pdb=" N LEU g 248 " --> pdb=" O TRP g 259 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE g 258 " --> pdb=" O ASP g 268 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 23 through 26 removed outlier: 6.697A pdb=" N LEU k 55 " --> pdb=" O VAL k 81 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARG k 83 " --> pdb=" O LEU k 55 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL k 57 " --> pdb=" O ARG k 83 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU k 80 " --> pdb=" O ASP k 105 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP k 208 " --> pdb=" O LEU k 184 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 337 through 340 removed outlier: 3.680A pdb=" N THR k 374 " --> pdb=" O THR k 484 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 388 through 392 removed outlier: 4.362A pdb=" N LEU k 388 " --> pdb=" O VAL k 452 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU k 451 " --> pdb=" O ILE k 459 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'z' and resid 181 through 183 removed outlier: 3.814A pdb=" N GLU z 181 " --> pdb=" O SER z 198 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER z 198 " --> pdb=" O GLU z 181 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA z 197 " --> pdb=" O ARG z 205 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET z 269 " --> pdb=" O VAL z 276 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER z 278 " --> pdb=" O PRO z 267 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'z' and resid 330 through 333 removed outlier: 3.819A pdb=" N HIS z 333 " --> pdb=" O GLY z 336 " (cutoff:3.500A) 1558 hydrogen bonds defined for protein. 4344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1172 hydrogen bonds 1884 hydrogen bond angles 0 basepair planarities 468 basepair parallelities 899 stacking parallelities Total time for adding SS restraints: 55.75 Time building geometry restraints manager: 17.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10825 1.32 - 1.44: 31422 1.44 - 1.57: 39569 1.57 - 1.70: 3270 1.70 - 1.82: 287 Bond restraints: 85373 Sorted by residual: bond pdb=" C GLN R 74 " pdb=" O GLN R 74 " ideal model delta sigma weight residual 1.235 1.292 -0.057 1.26e-02 6.30e+03 2.06e+01 bond pdb=" C SER y 325 " pdb=" N LEU y 326 " ideal model delta sigma weight residual 1.331 1.243 0.088 2.07e-02 2.33e+03 1.83e+01 bond pdb=" C ASN Y 85 " pdb=" N GLU Y 86 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.83e-02 1.25e+03 1.27e+01 bond pdb=" C ILE E 114 " pdb=" N THR E 115 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.52e+00 bond pdb=" C PRO y 58 " pdb=" N LEU y 59 " ideal model delta sigma weight residual 1.331 1.274 0.057 2.07e-02 2.33e+03 7.47e+00 ... (remaining 85368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 121248 3.25 - 6.50: 1797 6.50 - 9.75: 175 9.75 - 13.01: 18 13.01 - 16.26: 4 Bond angle restraints: 123242 Sorted by residual: angle pdb=" O3' G 21256 " pdb=" C3' G 21256 " pdb=" C2' G 21256 " ideal model delta sigma weight residual 109.50 125.76 -16.26 1.50e+00 4.44e-01 1.17e+02 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.49e+01 angle pdb=" N GLY L 41 " pdb=" CA GLY L 41 " pdb=" C GLY L 41 " ideal model delta sigma weight residual 112.49 119.90 -7.41 1.21e+00 6.83e-01 3.75e+01 angle pdb=" O3' G 21686 " pdb=" C3' G 21686 " pdb=" C2' G 21686 " ideal model delta sigma weight residual 113.70 122.46 -8.76 1.50e+00 4.44e-01 3.41e+01 angle pdb=" C4' C 21283 " pdb=" C3' C 21283 " pdb=" O3' C 21283 " ideal model delta sigma weight residual 113.00 104.35 8.65 1.50e+00 4.44e-01 3.33e+01 ... (remaining 123237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 49209 35.89 - 71.77: 4366 71.77 - 107.66: 493 107.66 - 143.54: 29 143.54 - 179.43: 31 Dihedral angle restraints: 54128 sinusoidal: 37160 harmonic: 16968 Sorted by residual: dihedral pdb=" C5' U 21308 " pdb=" C4' U 21308 " pdb=" C3' U 21308 " pdb=" O3' U 21308 " ideal model delta sinusoidal sigma weight residual 147.00 74.76 72.24 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" CA ASN F 165 " pdb=" C ASN F 165 " pdb=" N ILE F 166 " pdb=" CA ILE F 166 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA F 40 " pdb=" C ALA F 40 " pdb=" N VAL F 41 " pdb=" CA VAL F 41 " ideal model delta harmonic sigma weight residual -180.00 -130.38 -49.62 0 5.00e+00 4.00e-02 9.85e+01 ... (remaining 54125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 15037 0.169 - 0.339: 186 0.339 - 0.508: 10 0.508 - 0.678: 1 0.678 - 0.847: 1 Chirality restraints: 15235 Sorted by residual: chirality pdb=" C3' G 21256 " pdb=" C4' G 21256 " pdb=" O3' G 21256 " pdb=" C2' G 21256 " both_signs ideal model delta sigma weight residual False -2.74 -1.90 -0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" C3' U 21539 " pdb=" C4' U 21539 " pdb=" O3' U 21539 " pdb=" C2' U 21539 " both_signs ideal model delta sigma weight residual False -2.48 -1.86 -0.62 2.00e-01 2.50e+01 9.68e+00 chirality pdb=" C3' U 21308 " pdb=" C4' U 21308 " pdb=" O3' U 21308 " pdb=" C2' U 21308 " both_signs ideal model delta sigma weight residual False -2.74 -2.24 -0.50 2.00e-01 2.50e+01 6.27e+00 ... (remaining 15232 not shown) Planarity restraints: 9615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 73 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C LEU R 73 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU R 73 " 0.030 2.00e-02 2.50e+03 pdb=" N GLN R 74 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 495 " 0.053 2.00e-02 2.50e+03 2.71e-02 1.66e+01 pdb=" N1 U 2 495 " -0.057 2.00e-02 2.50e+03 pdb=" C2 U 2 495 " -0.004 2.00e-02 2.50e+03 pdb=" O2 U 2 495 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U 2 495 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U 2 495 " 0.009 2.00e-02 2.50e+03 pdb=" O4 U 2 495 " 0.017 2.00e-02 2.50e+03 pdb=" C5 U 2 495 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U 2 495 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 236 " -0.029 2.00e-02 2.50e+03 2.83e-02 1.40e+01 pdb=" CG PHE C 236 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 236 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE C 236 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 236 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 236 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 236 " -0.003 2.00e-02 2.50e+03 ... (remaining 9612 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 5164 2.69 - 3.25: 68402 3.25 - 3.80: 147010 3.80 - 4.35: 195032 4.35 - 4.90: 278828 Nonbonded interactions: 694436 Sorted by model distance: nonbonded pdb=" O TRP F 152 " pdb=" OG1 THR F 156 " model vdw 2.142 3.040 nonbonded pdb=" O2' C 21415 " pdb=" OD2 ASP T 132 " model vdw 2.143 3.040 nonbonded pdb=" O2 C 21279 " pdb=" N2 G 21318 " model vdw 2.173 2.496 nonbonded pdb=" O6 G 21722 " pdb=" O2 U 21812 " model vdw 2.184 2.432 nonbonded pdb=" O ARG F 71 " pdb=" OG SER F 75 " model vdw 2.185 3.040 ... (remaining 694431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.060 Extract box with map and model: 2.510 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 185.740 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.250 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 85373 Z= 0.596 Angle : 1.066 16.258 123242 Z= 0.546 Chirality : 0.061 0.847 15235 Planarity : 0.007 0.080 9615 Dihedral : 22.444 179.429 43158 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.78 % Favored : 92.10 % Rotamer: Outliers : 0.54 % Allowed : 10.09 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.74 (0.09), residues: 5811 helix: -2.78 (0.09), residues: 1767 sheet: -1.67 (0.16), residues: 944 loop : -2.58 (0.09), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP g 247 HIS 0.022 0.002 HIS H 126 PHE 0.065 0.003 PHE C 236 TYR 0.034 0.003 TYR C 248 ARG 0.018 0.001 ARG x 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 1029 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 MET cc_start: 0.7285 (mtp) cc_final: 0.6906 (mtp) REVERT: I 7 ASN cc_start: 0.7436 (t0) cc_final: 0.7071 (t0) REVERT: L 104 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7553 (tppt) REVERT: W 5 ASN cc_start: 0.7290 (t0) cc_final: 0.7082 (t0) REVERT: W 18 GLU cc_start: 0.7705 (tp30) cc_final: 0.7480 (mm-30) REVERT: W 88 LYS cc_start: 0.8372 (mttt) cc_final: 0.8159 (mppt) REVERT: X 114 ASP cc_start: 0.6804 (t70) cc_final: 0.6508 (t70) REVERT: e 41 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7467 (mtt180) REVERT: D 149 SER cc_start: 0.7956 (m) cc_final: 0.7750 (p) REVERT: P 28 MET cc_start: 0.2480 (mtm) cc_final: 0.1381 (tmm) REVERT: S 117 ILE cc_start: 0.4183 (mm) cc_final: 0.3586 (mp) REVERT: k 206 THR cc_start: 0.8637 (m) cc_final: 0.7969 (m) REVERT: k 231 ASN cc_start: 0.8226 (t0) cc_final: 0.7966 (t0) outliers start: 25 outliers final: 10 residues processed: 1047 average time/residue: 1.8547 time to fit residues: 2496.2782 Evaluate side-chains 757 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 747 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 21 TYR Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain Y residue 51 THR Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain d residue 53 ILE Chi-restraints excluded: chain g residue 113 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 0.0570 chunk 559 optimal weight: 10.0000 chunk 310 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 578 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 351 optimal weight: 0.9990 chunk 430 optimal weight: 1.9990 chunk 670 optimal weight: 5.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 83 ASN A 84 GLN A 215 GLN B 163 GLN C 272 HIS E 8 HIS E 17 HIS E 179 ASN E 209 HIS E 214 ASN G 13 GLN G 59 GLN G 177 GLN G 197 GLN H 97 GLN H 157 HIS H 165 ASN H 186 ASN I 84 ASN I 87 ASN I 138 ASN I 168 GLN J 75 ASN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 HIS N 90 HIS V 47 ASN X 23 HIS ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 110 HIS Y 63 HIS Y 89 HIS e 58 ASN x 210 HIS x 232 ASN y 118 HIS y 290 ASN y 348 GLN y 386 GLN D 174 HIS F 65 GLN F 83 ASN F 110 GLN F 114 ASN F 179 ASN F 186 ASN ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 HIS P 79 HIS Q 11 GLN Q 35 ASN Q 86 GLN Q 97 GLN S 120 HIS T 63 HIS T 83 GLN U 28 ASN Z 64 ASN Z 103 HIS Z 106 GLN c 29 GLN f 139 HIS g 20 GLN g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 237 ASN k 76 GLN k 78 HIS k 109 ASN k 135 ASN k 139 ASN k 163 ASN k 211 ASN k 235 ASN k 250 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.178887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.160977 restraints weight = 108292.067| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.45 r_work: 0.3797 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 85373 Z= 0.177 Angle : 0.681 15.922 123242 Z= 0.349 Chirality : 0.041 0.313 15235 Planarity : 0.005 0.105 9615 Dihedral : 23.450 179.610 32162 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -2.57 (0.10), residues: 5811 helix: -1.34 (0.11), residues: 1782 sheet: -1.23 (0.16), residues: 897 loop : -2.08 (0.10), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 132 HIS 0.010 0.001 HIS K 28 PHE 0.028 0.001 PHE R 111 TYR 0.022 0.001 TYR G 28 ARG 0.021 0.001 ARG U 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 872 time to evaluate : 4.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.7066 (tt0) cc_final: 0.6819 (tt0) REVERT: B 75 GLN cc_start: 0.7693 (tp40) cc_final: 0.7384 (tp40) REVERT: C 215 MET cc_start: 0.7690 (mtp) cc_final: 0.7297 (mtp) REVERT: E 198 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7532 (ttm170) REVERT: E 200 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7546 (mtt180) REVERT: J 130 ILE cc_start: 0.8803 (mt) cc_final: 0.8549 (mm) REVERT: O 83 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7666 (tm-30) REVERT: V 47 ASN cc_start: 0.7628 (t0) cc_final: 0.7308 (t0) REVERT: V 62 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6656 (ptm) REVERT: W 5 ASN cc_start: 0.7310 (t0) cc_final: 0.7078 (t0) REVERT: Y 47 MET cc_start: 0.8078 (mtp) cc_final: 0.7795 (ttm) REVERT: e 41 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7700 (mtt180) REVERT: y 309 HIS cc_start: 0.6963 (t70) cc_final: 0.6760 (t70) REVERT: P 28 MET cc_start: 0.2123 (mtm) cc_final: 0.1778 (tmm) REVERT: P 62 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.6215 (ttpt) REVERT: k 231 ASN cc_start: 0.8540 (t0) cc_final: 0.8255 (t160) outliers start: 133 outliers final: 33 residues processed: 951 average time/residue: 1.6367 time to fit residues: 2076.9793 Evaluate side-chains 753 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 717 time to evaluate : 4.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 413 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 471 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 595 optimal weight: 4.9990 chunk 309 optimal weight: 0.0040 chunk 63 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 704 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 293 optimal weight: 0.0980 chunk 137 optimal weight: 30.0000 chunk 482 optimal weight: 4.9990 overall best weight: 2.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS C 113 GLN C 235 ASN C 267 GLN G 146 ASN G 186 GLN G 197 GLN G 225 GLN H 97 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN I 168 GLN J 143 ASN L 83 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN X 46 HIS ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 110 HIS x 91 ASN y 129 HIS y 247 GLN D 174 HIS F 101 HIS K 42 ASN Q 80 GLN Q 142 GLN T 91 HIS g 62 HIS g 64 HIS g 76 GLN ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 135 ASN k 159 ASN k 211 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157456 restraints weight = 107755.573| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.49 r_work: 0.3752 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 85373 Z= 0.266 Angle : 0.680 11.979 123242 Z= 0.347 Chirality : 0.043 0.327 15235 Planarity : 0.005 0.058 9615 Dihedral : 23.305 179.203 32155 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 94.99 % Rotamer: Outliers : 4.08 % Allowed : 20.92 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -2.09 (0.10), residues: 5811 helix: -0.76 (0.12), residues: 1791 sheet: -1.01 (0.16), residues: 910 loop : -1.91 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP d 8 HIS 0.006 0.001 HIS F 101 PHE 0.028 0.002 PHE T 14 TYR 0.025 0.002 TYR G 28 ARG 0.015 0.001 ARG T 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 736 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5278 (mp0) REVERT: R 63 ARG cc_start: 0.6487 (tpp-160) cc_final: 0.6252 (mpt-90) REVERT: C 227 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6469 (ttt180) REVERT: E 198 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7464 (ttm170) REVERT: E 200 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7533 (mtt180) REVERT: I 53 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7856 (mttp) REVERT: I 61 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7260 (t0) REVERT: J 130 ILE cc_start: 0.8893 (mt) cc_final: 0.8637 (mm) REVERT: J 154 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: J 156 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7897 (p90) REVERT: L 121 GLN cc_start: 0.7632 (mt0) cc_final: 0.7334 (mt0) REVERT: O 83 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7563 (tm-30) REVERT: V 47 ASN cc_start: 0.7719 (t0) cc_final: 0.7419 (t0) REVERT: V 62 MET cc_start: 0.6953 (mtp) cc_final: 0.6532 (ptm) REVERT: W 5 ASN cc_start: 0.7447 (t0) cc_final: 0.7232 (t0) REVERT: e 41 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7727 (mtt180) REVERT: x 145 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7055 (mp-120) REVERT: y 307 HIS cc_start: 0.5601 (OUTLIER) cc_final: 0.5378 (p90) REVERT: y 309 HIS cc_start: 0.7127 (t70) cc_final: 0.6800 (t70) REVERT: y 386 GLN cc_start: 0.8020 (mt0) cc_final: 0.7557 (tt0) REVERT: D 116 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5729 (mtp-110) REVERT: D 189 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.6664 (tpt) REVERT: P 28 MET cc_start: 0.2455 (mtm) cc_final: 0.1604 (tmm) REVERT: k 190 CYS cc_start: 0.7479 (p) cc_final: 0.7254 (p) REVERT: k 231 ASN cc_start: 0.8657 (t0) cc_final: 0.8452 (t160) outliers start: 189 outliers final: 65 residues processed: 856 average time/residue: 1.5538 time to fit residues: 1788.3113 Evaluate side-chains 786 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 710 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 44 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain W residue 4 MET Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 119 ARG Chi-restraints excluded: chain x residue 145 GLN Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain T residue 59 SER Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 413 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 291 optimal weight: 5.9990 chunk 346 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 623 optimal weight: 30.0000 chunk 386 optimal weight: 0.0470 chunk 50 optimal weight: 8.9990 chunk 617 optimal weight: 10.0000 chunk 614 optimal weight: 5.9990 chunk 682 optimal weight: 1.9990 chunk 441 optimal weight: 20.0000 chunk 462 optimal weight: 40.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 208 HIS C 267 GLN G 197 GLN H 165 ASN I 168 GLN I 181 GLN J 143 ASN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN V 33 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN x 91 ASN y 247 GLN D 56 GLN D 174 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN Q 80 GLN T 91 HIS U 28 ASN Z 89 GLN g 62 HIS g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 109 ASN k 135 ASN k 189 ASN k 211 ASN k 436 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.174703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156032 restraints weight = 108026.136| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.56 r_work: 0.3728 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.006 0.057 85373 Z= 0.366 Angle : 0.732 14.030 123242 Z= 0.369 Chirality : 0.045 0.345 15235 Planarity : 0.005 0.077 9615 Dihedral : 23.306 179.580 32155 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 4.67 % Allowed : 21.98 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.87 (0.10), residues: 5811 helix: -0.49 (0.12), residues: 1784 sheet: -0.95 (0.16), residues: 916 loop : -1.80 (0.10), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 23 HIS 0.035 0.001 HIS F 101 PHE 0.026 0.002 PHE F 61 TYR 0.027 0.002 TYR Q 95 ARG 0.010 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 721 time to evaluate : 4.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 20 TYR cc_start: 0.6704 (m-80) cc_final: 0.6488 (m-80) REVERT: R 63 ARG cc_start: 0.6622 (tpp-160) cc_final: 0.6369 (mpt-90) REVERT: B 217 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8056 (tpp) REVERT: B 229 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6467 (mmm) REVERT: C 227 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6649 (ttt180) REVERT: E 198 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: G 103 ASP cc_start: 0.8017 (t0) cc_final: 0.7796 (t0) REVERT: I 53 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7883 (mttp) REVERT: I 61 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7332 (t0) REVERT: J 154 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: J 156 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.7931 (p90) REVERT: L 121 GLN cc_start: 0.7605 (mt0) cc_final: 0.7345 (mt0) REVERT: N 104 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7173 (ttm110) REVERT: O 37 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6827 (p90) REVERT: O 83 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7660 (tm-30) REVERT: V 47 ASN cc_start: 0.7873 (t0) cc_final: 0.7586 (t0) REVERT: V 62 MET cc_start: 0.7019 (mtp) cc_final: 0.6542 (ptm) REVERT: W 5 ASN cc_start: 0.7654 (t0) cc_final: 0.7422 (t0) REVERT: e 41 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7706 (mtt180) REVERT: y 307 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.5444 (p90) REVERT: y 309 HIS cc_start: 0.7264 (t70) cc_final: 0.6916 (t70) REVERT: y 386 GLN cc_start: 0.8042 (mt0) cc_final: 0.7574 (tt0) REVERT: D 116 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5987 (mtp-110) REVERT: P 28 MET cc_start: 0.2168 (mtm) cc_final: 0.1557 (tmm) REVERT: k 190 CYS cc_start: 0.7643 (p) cc_final: 0.7338 (p) outliers start: 216 outliers final: 96 residues processed: 865 average time/residue: 1.5397 time to fit residues: 1796.0785 Evaluate side-chains 794 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 686 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 44 LYS Chi-restraints excluded: chain R residue 49 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 156 HIS Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 37 PHE Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain O residue 143 LYS Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 98 ASP Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 39 GLU Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 119 ARG Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 389 ASP Chi-restraints excluded: chain y residue 391 THR Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 118 THR Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 116 ASP Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 312 VAL Chi-restraints excluded: chain k residue 19 GLU Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain k residue 103 VAL Chi-restraints excluded: chain k residue 424 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 59 optimal weight: 3.9990 chunk 315 optimal weight: 0.7980 chunk 453 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 299 optimal weight: 0.2980 chunk 672 optimal weight: 7.9990 chunk 245 optimal weight: 0.0980 chunk 597 optimal weight: 8.9990 chunk 380 optimal weight: 1.9990 chunk 480 optimal weight: 0.0670 chunk 377 optimal weight: 4.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 208 HIS C 267 GLN G 146 ASN G 197 GLN G 225 GLN H 165 ASN I 146 GLN I 168 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 33 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** y 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS D 174 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN P 32 GLN Q 80 GLN T 91 HIS ** U 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 HIS g 188 HIS k 135 ASN k 159 ASN k 163 ASN k 189 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.180122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.160669 restraints weight = 109319.387| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 0.49 r_work: 0.3790 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 85373 Z= 0.148 Angle : 0.614 12.564 123242 Z= 0.311 Chirality : 0.038 0.281 15235 Planarity : 0.004 0.059 9615 Dihedral : 23.167 179.678 32155 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 3.13 % Allowed : 23.88 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -1.39 (0.11), residues: 5811 helix: 0.03 (0.12), residues: 1788 sheet: -0.75 (0.16), residues: 927 loop : -1.56 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP F 23 HIS 0.008 0.001 HIS B 208 PHE 0.037 0.001 PHE T 14 TYR 0.028 0.001 TYR G 28 ARG 0.010 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 746 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5428 (tp30) REVERT: A 185 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8290 (mtt) REVERT: B 217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: B 225 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7373 (mt) REVERT: C 145 LYS cc_start: 0.7348 (mtpp) cc_final: 0.7146 (mttt) REVERT: C 227 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6469 (ttm170) REVERT: I 61 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7227 (t0) REVERT: J 50 LEU cc_start: 0.8664 (tp) cc_final: 0.8415 (tp) REVERT: J 130 ILE cc_start: 0.8789 (mt) cc_final: 0.8492 (mm) REVERT: J 154 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: L 121 GLN cc_start: 0.7479 (mt0) cc_final: 0.7231 (mt0) REVERT: N 86 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: O 83 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7284 (tm-30) REVERT: O 149 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6538 (mtp180) REVERT: V 38 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6975 (mt-10) REVERT: V 47 ASN cc_start: 0.7710 (t0) cc_final: 0.7510 (t0) REVERT: V 62 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6625 (ptm) REVERT: b 72 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7335 (ttm170) REVERT: e 41 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7672 (mtt180) REVERT: x 145 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7035 (mp-120) REVERT: y 309 HIS cc_start: 0.7117 (t70) cc_final: 0.6720 (t70) REVERT: D 162 ASP cc_start: 0.6808 (t0) cc_final: 0.6574 (m-30) REVERT: P 28 MET cc_start: 0.2006 (mtm) cc_final: 0.1508 (tmm) outliers start: 145 outliers final: 48 residues processed: 835 average time/residue: 1.5535 time to fit residues: 1725.8613 Evaluate side-chains 747 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 688 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 149 ARG Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 145 GLN Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain k residue 103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 212 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 307 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 505 optimal weight: 8.9990 chunk 645 optimal weight: 0.9980 chunk 375 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 705 optimal weight: 20.0000 chunk 585 optimal weight: 0.0970 chunk 709 optimal weight: 40.0000 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 163 GLN B 208 HIS G 197 GLN G 225 GLN H 112 ASN I 87 ASN I 146 GLN I 168 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 243 ASN ** y 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS D 174 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS U 28 ASN g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 135 ASN k 163 ASN k 189 ASN k 200 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158770 restraints weight = 108293.037| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 0.50 r_work: 0.3761 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 85373 Z= 0.206 Angle : 0.630 11.793 123242 Z= 0.319 Chirality : 0.040 0.290 15235 Planarity : 0.004 0.060 9615 Dihedral : 23.071 177.966 32155 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 3.22 % Allowed : 24.83 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % 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: -1.24 (0.11), residues: 5811 helix: 0.19 (0.13), residues: 1792 sheet: -0.71 (0.16), residues: 932 loop : -1.48 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 23 HIS 0.013 0.001 HIS F 101 PHE 0.021 0.001 PHE Q 13 TYR 0.025 0.001 TYR G 28 ARG 0.010 0.000 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 705 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 18 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5480 (tp30) REVERT: C 227 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6447 (ttt180) REVERT: E 198 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: I 61 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7283 (t0) REVERT: J 130 ILE cc_start: 0.8822 (mt) cc_final: 0.8584 (mm) REVERT: J 154 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: L 121 GLN cc_start: 0.7480 (mt0) cc_final: 0.7277 (mt0) REVERT: V 38 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6993 (mt-10) REVERT: V 62 MET cc_start: 0.7036 (mtp) cc_final: 0.6620 (ptm) REVERT: W 5 ASN cc_start: 0.7453 (t0) cc_final: 0.7247 (t0) REVERT: b 72 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7438 (ttm170) REVERT: e 41 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7731 (mtt180) REVERT: D 162 ASP cc_start: 0.6882 (t0) cc_final: 0.6594 (m-30) REVERT: P 28 MET cc_start: 0.1976 (mtm) cc_final: 0.1567 (tmt) REVERT: c 29 GLN cc_start: 0.4148 (tp-100) cc_final: 0.2838 (mp10) REVERT: k 190 CYS cc_start: 0.7490 (p) cc_final: 0.7222 (p) REVERT: k 197 ASP cc_start: 0.6956 (t0) cc_final: 0.6610 (t0) REVERT: k 236 LYS cc_start: 0.7277 (mmmm) cc_final: 0.7001 (mmmm) outliers start: 149 outliers final: 71 residues processed: 802 average time/residue: 1.4540 time to fit residues: 1593.1564 Evaluate side-chains 756 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 679 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 104 ARG Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 218 ILE Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 312 VAL Chi-restraints excluded: chain k residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 545 optimal weight: 6.9990 chunk 391 optimal weight: 4.9990 chunk 665 optimal weight: 0.0770 chunk 715 optimal weight: 40.0000 chunk 307 optimal weight: 0.4980 chunk 62 optimal weight: 20.0000 chunk 586 optimal weight: 40.0000 chunk 321 optimal weight: 9.9990 chunk 732 optimal weight: 0.5980 chunk 204 optimal weight: 7.9990 chunk 578 optimal weight: 8.9990 overall best weight: 2.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 208 HIS G 146 ASN G 197 GLN H 126 HIS I 146 GLN I 168 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN V 47 ASN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 243 ASN ** y 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS D 174 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** U 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 135 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.176551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157468 restraints weight = 107672.722| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.52 r_work: 0.3746 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 85373 Z= 0.259 Angle : 0.665 23.352 123242 Z= 0.334 Chirality : 0.041 0.307 15235 Planarity : 0.005 0.059 9615 Dihedral : 23.068 178.982 32155 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.37 % Allowed : 25.31 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.18 (0.11), residues: 5811 helix: 0.25 (0.12), residues: 1792 sheet: -0.67 (0.16), residues: 932 loop : -1.45 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 69 HIS 0.013 0.001 HIS R 56 PHE 0.033 0.002 PHE T 14 TYR 0.027 0.002 TYR G 28 ARG 0.011 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 708 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 227 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6612 (ttt180) REVERT: E 198 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7515 (ttm170) REVERT: H 25 GLN cc_start: 0.5252 (tp-100) cc_final: 0.4973 (tp40) REVERT: I 61 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7269 (t0) REVERT: J 130 ILE cc_start: 0.8926 (mt) cc_final: 0.8683 (mm) REVERT: J 154 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: J 158 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: L 121 GLN cc_start: 0.7506 (mt0) cc_final: 0.7300 (mt0) REVERT: V 38 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7080 (mt-10) REVERT: V 47 ASN cc_start: 0.7705 (t0) cc_final: 0.7467 (t0) REVERT: V 62 MET cc_start: 0.7034 (mtp) cc_final: 0.6573 (ptm) REVERT: W 5 ASN cc_start: 0.7544 (t0) cc_final: 0.7299 (t0) REVERT: W 51 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7288 (mt-10) REVERT: X 73 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: b 72 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7434 (ttm170) REVERT: e 41 ARG cc_start: 0.8051 (mtt180) cc_final: 0.7718 (mtt180) REVERT: y 307 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.5066 (p90) REVERT: y 309 HIS cc_start: 0.7078 (t70) cc_final: 0.6770 (t70) REVERT: P 28 MET cc_start: 0.1925 (mtm) cc_final: 0.1632 (tmm) REVERT: c 29 GLN cc_start: 0.4061 (tp-100) cc_final: 0.2753 (mp10) REVERT: g 113 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.4905 (t80) REVERT: k 197 ASP cc_start: 0.7012 (t0) cc_final: 0.6635 (t0) outliers start: 156 outliers final: 86 residues processed: 816 average time/residue: 1.3318 time to fit residues: 1462.2562 Evaluate side-chains 780 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 685 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 44 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain J residue 154 GLN Chi-restraints excluded: chain J residue 158 ASP Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 191 HIS Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 312 VAL Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 103 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 346 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 557 optimal weight: 50.0000 chunk 421 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 665 optimal weight: 0.0270 chunk 63 optimal weight: 6.9990 chunk 515 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 624 optimal weight: 9.9990 overall best weight: 2.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 208 HIS G 146 ASN G 163 ASN I 116 HIS I 146 GLN I 168 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN ** y 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 28 HIS D 174 HIS ** K 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** U 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 64 HIS ** g 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 436 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.176440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157642 restraints weight = 107878.040| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.50 r_work: 0.3759 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 85373 Z= 0.268 Angle : 0.675 18.273 123242 Z= 0.339 Chirality : 0.042 0.321 15235 Planarity : 0.005 0.062 9615 Dihedral : 23.054 178.995 32154 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 3.31 % Allowed : 26.09 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.13 (0.11), residues: 5811 helix: 0.30 (0.12), residues: 1791 sheet: -0.63 (0.17), residues: 925 loop : -1.43 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 64 HIS 0.013 0.001 HIS R 56 PHE 0.025 0.002 PHE D 17 TYR 0.029 0.002 TYR G 28 ARG 0.012 0.001 ARG H 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11622 Ramachandran restraints generated. 5811 Oldfield, 0 Emsley, 5811 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 705 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6887 (mm-30) REVERT: C 227 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7151 (ttm170) REVERT: E 198 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7487 (ttm170) REVERT: I 61 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7266 (t0) REVERT: J 130 ILE cc_start: 0.8904 (mt) cc_final: 0.8680 (mm) REVERT: N 86 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6505 (tt0) REVERT: O 83 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7730 (tp-100) REVERT: V 38 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7109 (mt-10) REVERT: V 47 ASN cc_start: 0.7722 (t0) cc_final: 0.7506 (t0) REVERT: V 62 MET cc_start: 0.7043 (mtp) cc_final: 0.6588 (ptm) REVERT: W 5 ASN cc_start: 0.7531 (t0) cc_final: 0.7330 (t0) REVERT: X 73 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: b 72 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7435 (ttm170) REVERT: e 41 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7722 (mtt180) REVERT: y 307 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.5192 (p90) REVERT: y 309 HIS cc_start: 0.7164 (t70) cc_final: 0.6776 (t70) REVERT: F 88 MET cc_start: 0.6602 (mmt) cc_final: 0.6316 (mmp) REVERT: P 28 MET cc_start: 0.1944 (mtm) cc_final: 0.1622 (tmt) REVERT: c 29 GLN cc_start: 0.4068 (tp-100) cc_final: 0.2836 (mp10) REVERT: g 113 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.4921 (t80) REVERT: k 197 ASP cc_start: 0.6996 (t0) cc_final: 0.6631 (t0) outliers start: 153 outliers final: 93 residues processed: 809 average time/residue: 1.3551 time to fit residues: 1473.8949 Evaluate side-chains 784 residues out of total 5095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 683 time to evaluate : 4.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 44 LYS Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 198 ARG Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 100 CYS Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 89 ARG Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 86 GLU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 54 CYS Chi-restraints excluded: chain O residue 85 CYS Chi-restraints excluded: chain O residue 88 LEU Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 65 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 84 LYS Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 73 GLN Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 102 THR Chi-restraints excluded: chain b residue 72 ARG Chi-restraints excluded: chain e residue 5 SER Chi-restraints excluded: chain x residue 168 VAL Chi-restraints excluded: chain x residue 207 VAL Chi-restraints excluded: chain x residue 230 LEU Chi-restraints excluded: chain y residue 116 ILE Chi-restraints excluded: chain y residue 123 LEU Chi-restraints excluded: chain y residue 210 THR Chi-restraints excluded: chain y residue 214 ILE Chi-restraints excluded: chain y residue 307 HIS Chi-restraints excluded: chain y residue 359 THR Chi-restraints excluded: chain y residue 391 THR Chi-restraints excluded: chain y residue 400 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 65 THR Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain Z residue 107 VAL Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 198 VAL Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 252 THR Chi-restraints excluded: chain g residue 312 VAL Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 103 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5938 > 50: distance: 16 - 24: 7.998 distance: 24 - 25: 9.251 distance: 25 - 26: 18.085 distance: 25 - 28: 20.381 distance: 26 - 27: 19.769 distance: 26 - 33: 22.268 distance: 28 - 29: 22.261 distance: 30 - 31: 12.516 distance: 30 - 32: 7.124 distance: 33 - 34: 6.567 distance: 34 - 35: 4.654 distance: 34 - 37: 4.496 distance: 35 - 36: 34.986 distance: 35 - 39: 22.888 distance: 39 - 40: 21.545 distance: 39 - 45: 19.531 distance: 40 - 41: 28.402 distance: 40 - 43: 22.720 distance: 41 - 42: 15.638 distance: 41 - 46: 9.065 distance: 43 - 44: 35.483 distance: 44 - 45: 25.514 distance: 46 - 47: 38.681 distance: 47 - 48: 40.147 distance: 47 - 50: 35.751 distance: 48 - 49: 7.444 distance: 48 - 52: 16.158 distance: 52 - 53: 9.916 distance: 53 - 54: 7.141 distance: 53 - 56: 13.858 distance: 54 - 55: 31.077 distance: 54 - 60: 24.186 distance: 56 - 57: 10.387 distance: 57 - 58: 17.754 distance: 57 - 59: 7.568 distance: 60 - 61: 10.219 distance: 61 - 62: 8.460 distance: 61 - 64: 4.517 distance: 62 - 63: 14.227 distance: 62 - 69: 7.402 distance: 64 - 65: 18.177 distance: 65 - 66: 9.576 distance: 66 - 67: 9.115 distance: 66 - 68: 16.591 distance: 69 - 70: 26.099 distance: 70 - 71: 6.688 distance: 70 - 73: 22.079 distance: 71 - 72: 27.759 distance: 71 - 75: 20.701 distance: 73 - 74: 12.386 distance: 75 - 76: 20.444 distance: 76 - 77: 14.654 distance: 79 - 80: 4.185 distance: 80 - 81: 37.782 distance: 80 - 83: 10.173 distance: 81 - 82: 18.810 distance: 81 - 84: 9.734 distance: 84 - 85: 18.804 distance: 85 - 86: 24.184 distance: 86 - 87: 8.438 distance: 86 - 88: 28.918