Starting phenix.real_space_refine on Thu Mar 14 21:01:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eui_24423/03_2024/8eui_24423.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3131 5.49 5 S 159 5.16 5 C 65287 2.51 5 N 22812 2.21 5 O 31502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "N GLU 160": "OE1" <-> "OE2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "T GLU 21": "OE1" <-> "OE2" Residue "T GLU 86": "OE1" <-> "OE2" Residue "T GLU 113": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "X GLU 69": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X GLU 105": "OE1" <-> "OE2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "d GLU 63": "OE1" <-> "OE2" Residue "d GLU 107": "OE1" <-> "OE2" Residue "e GLU 80": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "h GLU 110": "OE1" <-> "OE2" Residue "i GLU 22": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "m ASP 644": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 122892 Number of models: 1 Model: "" Number of chains: 47 Chain: "1" Number of atoms: 61093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2855, 61093 Classifications: {'RNA': 2855} Modifications used: {'rna2p_pur': 311, 'rna2p_pyr': 190, 'rna3p_pur': 1293, 'rna3p_pyr': 1061} Link IDs: {'rna2p': 501, 'rna3p': 2353} Chain breaks: 32 Chain: "2" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3354 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 17, 'rna3p_pur': 61, 'rna3p_pyr': 62} Link IDs: {'rna2p': 34, 'rna3p': 123} Chain: "3" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1042 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "8" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 437 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "9" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2519 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 58, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 106} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1858 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3003 Classifications: {'peptide': 377} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 360} Chain: "C" Number of atoms: 2795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2795 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 340} Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2287 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1415 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 168} Chain: "F" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1745 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "G" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1804 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 217} Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 862 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 281 Chain: "I" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1354 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "J" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1359 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "K" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 695 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1612 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1676 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 190} Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1369 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain breaks: 1 Chain: "Q" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1487 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 178} Chain: "R" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1229 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "T" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1289 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Link IDs: {'TRANS': 97} Chain: "V" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1015 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "X" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "Z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "a" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1169 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 138} Chain: "b" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 471 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 712 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "e" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 939 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "g" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 861 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 767 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "j" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 80} Chain: "k" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 564 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "m" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3376 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 393} Chain breaks: 7 Chain: "n" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2966 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 342} Chain breaks: 4 Chain: "o" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "p" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 1401 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 851 Unresolved non-hydrogen angles: 1110 Unresolved non-hydrogen dihedrals: 724 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 9, 'ASP:plan': 22, 'PHE:plan': 10, 'GLU:plan': 8, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 443 Chain: "u" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 493 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "j" 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 A09UY SG CYS j 19 130.478 145.693 163.027 1.00 0.00 S ATOM A09VQ SG CYS j 22 132.990 146.318 160.154 1.00 6.74 S ATOM A09YE SG CYS j 34 131.440 143.006 160.591 1.00 0.00 S ATOM A09YV SG CYS j 37 133.997 144.095 163.112 1.00 0.00 S Time building chain proxies: 45.66, per 1000 atoms: 0.37 Number of scatterers: 122892 At special positions: 0 Unit cell: (241.68, 215.18, 277.72, 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 1 29.99 S 159 16.00 P 3131 15.00 O 31502 8.00 N 22812 7.00 C 65287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.96 Conformation dependent library (CDL) restraints added in 8.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13360 Finding SS restraints... Secondary structure from input PDB file: 249 helices and 84 sheets defined 37.1% alpha, 17.3% beta 890 base pairs and 1774 stacking pairs defined. Time for finding SS restraints: 39.89 Creating SS restraints... Processing helix chain '3' and resid 3 through 11 Processing helix chain '3' and resid 72 through 77 removed outlier: 4.649A pdb=" N TRP 3 77 " --> pdb=" O PRO 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 99 removed outlier: 4.734A pdb=" N TYR 3 99 " --> pdb=" O GLN 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 103 through 124 removed outlier: 4.760A pdb=" N ARG 3 107 " --> pdb=" O ARG 3 103 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 20 Processing helix chain '8' and resid 24 through 29 removed outlier: 4.099A pdb=" N ARG 8 28 " --> pdb=" O PRO 8 24 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 24 through 29' Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.942A pdb=" N GLN A 16 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.862A pdb=" N LYS A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.115A pdb=" N VAL A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.712A pdb=" N THR B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.506A pdb=" N GLN B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 132 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.060A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 3.626A pdb=" N LYS C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.446A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.877A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.859A pdb=" N TYR D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 191 through 200 Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.555A pdb=" N TYR D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 removed outlier: 3.521A pdb=" N TYR D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 removed outlier: 3.730A pdb=" N ASP D 229 " --> pdb=" O GLY D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.678A pdb=" N LYS D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'E' and resid 85 through 90 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 174 through 180 Processing helix chain 'F' and resid 38 through 80 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.567A pdb=" N VAL F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL F 137 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.175A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 198 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 240 through 250 removed outlier: 4.241A pdb=" N GLY F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 50 Processing helix chain 'G' and resid 53 through 69 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.790A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.516A pdb=" N VAL G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 121 through 126' Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.584A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 182 through 190 Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 225 through 230 Processing helix chain 'G' and resid 239 through 251 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.564A pdb=" N CYS H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.531A pdb=" N GLY H 117 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'I' and resid 62 through 81 Processing helix chain 'I' and resid 144 through 157 removed outlier: 4.126A pdb=" N TYR I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'I' and resid 205 through 211 Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 27 through 42 Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.528A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 136 through 141 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 155 through 168 Processing helix chain 'K' and resid 8 through 15 removed outlier: 3.731A pdb=" N LYS K 13 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 35 removed outlier: 4.364A pdb=" N VAL K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 92 Processing helix chain 'L' and resid 18 through 20 No H-bonds generated for 'chain 'L' and resid 18 through 20' Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.932A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'L' and resid 148 through 153 Processing helix chain 'L' and resid 167 through 172 Processing helix chain 'L' and resid 174 through 188 Processing helix chain 'L' and resid 188 through 203 Processing helix chain 'M' and resid 70 through 81 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.217A pdb=" N GLN M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 16 through 33 Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 75 through 79 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.662A pdb=" N ASN N 181 " --> pdb=" O HIS N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 194 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 61 removed outlier: 3.837A pdb=" N LYS O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 99 Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.211A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 124 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 147 Processing helix chain 'O' and resid 150 through 186 removed outlier: 3.616A pdb=" N GLU O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA O 185 " --> pdb=" O SER O 181 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 192 removed outlier: 3.702A pdb=" N LYS O 191 " --> pdb=" O PRO O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 77 removed outlier: 3.568A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS P 74 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 168 through 183 Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 53 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'Q' and resid 144 through 148 removed outlier: 3.945A pdb=" N ARG Q 148 " --> pdb=" O LYS Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 154 removed outlier: 3.925A pdb=" N HIS Q 153 " --> pdb=" O GLU Q 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'R' and resid 60 through 72 Processing helix chain 'R' and resid 77 through 81 removed outlier: 3.863A pdb=" N ARG R 81 " --> pdb=" O TYR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 113 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 150 Processing helix chain 'S' and resid 32 through 48 Processing helix chain 'S' and resid 97 through 114 Processing helix chain 'S' and resid 130 through 134 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'T' and resid 26 through 32 removed outlier: 3.724A pdb=" N THR T 29 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS T 32 " --> pdb=" O THR T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 123 Processing helix chain 'U' and resid 16 through 22 Processing helix chain 'U' and resid 26 through 38 Processing helix chain 'U' and resid 39 through 43 removed outlier: 3.797A pdb=" N GLY U 42 " --> pdb=" O LYS U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 85 removed outlier: 3.640A pdb=" N PHE U 81 " --> pdb=" O LEU U 77 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS U 83 " --> pdb=" O LYS U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 8 Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'X' and resid 57 through 61 Processing helix chain 'X' and resid 68 through 79 removed outlier: 3.612A pdb=" N ASN X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 103 Processing helix chain 'X' and resid 130 through 139 removed outlier: 3.527A pdb=" N VAL X 134 " --> pdb=" O ASP X 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.304A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Z' and resid 58 through 67 Processing helix chain 'Z' and resid 97 through 103 Processing helix chain 'Z' and resid 103 through 125 Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 65 through 69 Processing helix chain 'a' and resid 78 through 82 Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 130 through 140 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'b' and resid 36 through 61 Processing helix chain 'c' and resid 24 through 35 Processing helix chain 'c' and resid 40 through 51 removed outlier: 3.546A pdb=" N THR c 44 " --> pdb=" O GLY c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 78 Processing helix chain 'c' and resid 87 through 96 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'e' and resid 37 through 42 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 Processing helix chain 'e' and resid 82 through 84 No H-bonds generated for 'chain 'e' and resid 82 through 84' Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 46 removed outlier: 4.198A pdb=" N PHE f 44 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR f 45 " --> pdb=" O GLU f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.809A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 65 removed outlier: 3.508A pdb=" N LEU g 65 " --> pdb=" O PHE g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 71 removed outlier: 3.638A pdb=" N LYS g 70 " --> pdb=" O SER g 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR g 71 " --> pdb=" O HIS g 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 66 through 71' Processing helix chain 'g' and resid 81 through 108 removed outlier: 3.948A pdb=" N LEU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 10 Processing helix chain 'h' and resid 12 through 37 Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.012A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 removed outlier: 3.637A pdb=" N LYS i 28 " --> pdb=" O SER i 25 " (cutoff:3.500A) Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 97 Processing helix chain 'j' and resid 6 through 11 removed outlier: 3.516A pdb=" N ARG j 11 " --> pdb=" O PHE j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.887A pdb=" N ARG j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 76 removed outlier: 3.679A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 Processing helix chain 'k' and resid 50 through 61 Processing helix chain 'm' and resid 228 through 240 Processing helix chain 'm' and resid 328 through 343 removed outlier: 3.680A pdb=" N TYR m 341 " --> pdb=" O CYS m 337 " (cutoff:3.500A) Processing helix chain 'm' and resid 364 through 368 removed outlier: 3.897A pdb=" N GLU m 367 " --> pdb=" O THR m 364 " (cutoff:3.500A) Processing helix chain 'm' and resid 483 through 492 removed outlier: 3.673A pdb=" N ILE m 487 " --> pdb=" O SER m 483 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU m 492 " --> pdb=" O GLU m 488 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 15 Processing helix chain 'n' and resid 19 through 27 Processing helix chain 'n' and resid 29 through 40 Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 66 through 74 removed outlier: 4.211A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 97 removed outlier: 4.099A pdb=" N GLN n 79 " --> pdb=" O GLU n 75 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 109 Processing helix chain 'n' and resid 115 through 123 Processing helix chain 'n' and resid 125 through 132 Processing helix chain 'n' and resid 133 through 144 Processing helix chain 'n' and resid 153 through 175 Processing helix chain 'n' and resid 215 through 241 removed outlier: 3.606A pdb=" N PHE n 232 " --> pdb=" O ALA n 228 " (cutoff:3.500A) Processing helix chain 'n' and resid 365 through 375 Processing helix chain 'n' and resid 420 through 431 removed outlier: 3.729A pdb=" N VAL n 424 " --> pdb=" O GLN n 420 " (cutoff:3.500A) Processing helix chain 'n' and resid 553 through 559 Processing helix chain 'n' and resid 569 through 576 removed outlier: 4.117A pdb=" N TYR n 573 " --> pdb=" O GLN n 569 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 48 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 Processing helix chain 'u' and resid 52 through 59 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 52 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.679A pdb=" N LYS A 46 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA A 61 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL A 44 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ARG A 63 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY A 42 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.543A pdb=" N LEU A 101 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 146 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N HIS A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS A 144 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.045A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 95 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.045A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.622A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB1, first strand: chain 'C' and resid 17 through 23 removed outlier: 6.232A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 10 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'D' and resid 72 through 79 removed outlier: 7.001A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N CYS D 62 " --> pdb=" O HIS D 77 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N HIS D 79 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 60 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AB6, first strand: chain 'E' and resid 94 through 97 removed outlier: 6.903A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.850A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 212 through 213 removed outlier: 3.831A pdb=" N ASN F 120 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AC1, first strand: chain 'G' and resid 133 through 134 removed outlier: 6.237A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 7 through 12 removed outlier: 3.578A pdb=" N GLU H 45 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.064A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 130 through 133 removed outlier: 6.700A pdb=" N ARG H 87 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG H 182 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 178 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC6, first strand: chain 'I' and resid 35 through 37 removed outlier: 3.841A pdb=" N GLN I 133 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU I 52 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER I 137 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG I 139 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU I 48 " --> pdb=" O ARG I 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 58 through 61 Processing sheet with id=AC8, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AC9, first strand: chain 'J' and resid 46 through 49 removed outlier: 5.104A pdb=" N ILE J 14 " --> pdb=" O ASP J 132 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP J 132 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 90 through 92 removed outlier: 6.771A pdb=" N LEU J 91 " --> pdb=" O LEU J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'K' and resid 47 through 51 removed outlier: 6.779A pdb=" N ILE K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 22 through 24 removed outlier: 5.977A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD5, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD6, first strand: chain 'M' and resid 7 through 8 removed outlier: 3.505A pdb=" N PHE S 149 " --> pdb=" O VAL M 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.433A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE M 61 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU M 15 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR M 59 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.643A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 7 through 11 removed outlier: 5.851A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE2, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.522A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'P' and resid 128 through 131 removed outlier: 3.731A pdb=" N ARG P 135 " --> pdb=" O ARG P 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.151A pdb=" N ILE Q 61 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 61 through 62 removed outlier: 6.151A pdb=" N ILE Q 61 " --> pdb=" O THR Q 89 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR Q 81 " --> pdb=" O VAL Q 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE8, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.157A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 89 through 95 removed outlier: 4.371A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 83 through 92 removed outlier: 3.548A pdb=" N ARG T 83 " --> pdb=" O VAL T 80 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU T 75 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL T 64 " --> pdb=" O LEU T 75 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N TYR T 77 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLY T 62 " --> pdb=" O TYR T 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 51 through 54 removed outlier: 3.751A pdb=" N ALA U 62 " --> pdb=" O SER U 54 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 103 " --> pdb=" O ASP U 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'V' and resid 24 through 27 removed outlier: 7.123A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS V 65 " --> pdb=" O ASN V 35 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA V 101 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 87 through 88 removed outlier: 5.918A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR V 96 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.479A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'X' and resid 62 through 65 removed outlier: 3.680A pdb=" N LYS X 119 " --> pdb=" O VAL X 85 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF9, first strand: chain 'Y' and resid 93 through 98 removed outlier: 6.772A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS Y 68 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL Y 84 " --> pdb=" O GLU Y 66 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N GLU Y 66 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR Y 56 " --> pdb=" O ILE Y 105 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE Y 105 " --> pdb=" O THR Y 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.832A pdb=" N LYS Z 69 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS Z 40 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL Z 42 " --> pdb=" O LEU Z 26 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL Z 46 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS Z 22 " --> pdb=" O VAL Z 46 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 72 through 73 Processing sheet with id=AG3, first strand: chain 'a' and resid 100 through 102 Processing sheet with id=AG4, first strand: chain 'c' and resid 37 through 39 removed outlier: 6.396A pdb=" N ILE c 56 " --> pdb=" O HIS c 82 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 54 through 56 Processing sheet with id=AG6, first strand: chain 'e' and resid 69 through 73 removed outlier: 5.920A pdb=" N LYS e 69 " --> pdb=" O ALA e 90 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU e 92 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE e 71 " --> pdb=" O GLU e 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.693A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.320A pdb=" N ARG g 19 " --> pdb=" O ILE g 35 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AH1, first strand: chain 'k' and resid 3 through 4 removed outlier: 6.624A pdb=" N ARG k 3 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL k 47 " --> pdb=" O ARG k 3 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER k 22 " --> pdb=" O ARG k 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'm' and resid 388 through 391 Processing sheet with id=AH3, first strand: chain 'm' and resid 452 through 457 removed outlier: 3.630A pdb=" N SER m 454 " --> pdb=" O ALA m 469 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA m 523 " --> pdb=" O PHE m 476 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'm' and resid 533 through 536 Processing sheet with id=AH5, first strand: chain 'm' and resid 576 through 581 removed outlier: 6.675A pdb=" N ALA m 591 " --> pdb=" O GLN m 577 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL m 579 " --> pdb=" O LEU m 589 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU m 589 " --> pdb=" O VAL m 579 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE m 581 " --> pdb=" O TYR m 587 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR m 587 " --> pdb=" O PHE m 581 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR m 595 " --> pdb=" O THR m 592 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL m 596 " --> pdb=" O THR m 609 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR m 609 " --> pdb=" O VAL m 596 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE m 598 " --> pdb=" O VAL m 607 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'm' and resid 617 through 622 Processing sheet with id=AH7, first strand: chain 'm' and resid 660 through 665 removed outlier: 6.016A pdb=" N VAL m 681 " --> pdb=" O ILE m 703 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE m 703 " --> pdb=" O VAL m 681 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL m 683 " --> pdb=" O LEU m 701 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'm' and resid 717 through 720 removed outlier: 3.630A pdb=" N SER m 717 " --> pdb=" O ALA m 730 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 16 through 18 Processing sheet with id=AI1, first strand: chain 'n' and resid 177 through 182 removed outlier: 6.109A pdb=" N LEU n 177 " --> pdb=" O GLU n 192 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU n 192 " --> pdb=" O LEU n 177 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'n' and resid 379 through 381 removed outlier: 6.566A pdb=" N PHE n 358 " --> pdb=" O GLY n 381 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR n 357 " --> pdb=" O HIS n 401 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE n 403 " --> pdb=" O THR n 357 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE n 359 " --> pdb=" O ILE n 403 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AI4, first strand: chain 'o' and resid 7 through 12 removed outlier: 3.651A pdb=" N LYS o 19 " --> pdb=" O CYS o 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL o 68 " --> pdb=" O LEU o 85 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'p' and resid 96 through 102 removed outlier: 6.627A pdb=" N ILE p 430 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER p 100 " --> pdb=" O LEU p 428 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU p 428 " --> pdb=" O SER p 100 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN p 427 " --> pdb=" O GLY p 423 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY p 423 " --> pdb=" O GLN p 427 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY p 418 " --> pdb=" O TRP p 413 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP p 413 " --> pdb=" O GLY p 418 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL p 420 " --> pdb=" O VAL p 411 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL p 411 " --> pdb=" O VAL p 420 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY p 422 " --> pdb=" O PHE p 409 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'p' and resid 107 through 112 Processing sheet with id=AI7, first strand: chain 'p' and resid 146 through 151 removed outlier: 6.544A pdb=" N ALA p 161 " --> pdb=" O LYS p 147 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA p 149 " --> pdb=" O LEU p 159 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU p 159 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP p 151 " --> pdb=" O SER p 157 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N SER p 157 " --> pdb=" O TRP p 151 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS p 166 " --> pdb=" O SER p 162 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE p 167 " --> pdb=" O LEU p 192 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU p 192 " --> pdb=" O ILE p 167 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N HIS p 169 " --> pdb=" O GLN p 190 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'p' and resid 200 through 203 removed outlier: 4.010A pdb=" N THR p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'p' and resid 272 through 277 removed outlier: 4.186A pdb=" N GLY p 288 " --> pdb=" O THR p 292 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR p 292 " --> pdb=" O GLY p 288 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP p 305 " --> pdb=" O THR p 295 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP p 297 " --> pdb=" O ASN p 303 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN p 303 " --> pdb=" O ASP p 297 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'p' and resid 313 through 319 removed outlier: 6.453A pdb=" N GLY p 328 " --> pdb=" O LEU p 314 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL p 316 " --> pdb=" O ILE p 326 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE p 326 " --> pdb=" O VAL p 316 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS p 318 " --> pdb=" O LEU p 324 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU p 324 " --> pdb=" O LYS p 318 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS p 333 " --> pdb=" O SER p 329 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'p' and resid 358 through 363 removed outlier: 6.705A pdb=" N VAL p 374 " --> pdb=" O SER p 359 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU p 361 " --> pdb=" O ALA p 372 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA p 372 " --> pdb=" O LEU p 361 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA p 363 " --> pdb=" O MET p 370 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N MET p 370 " --> pdb=" O ALA p 363 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'u' and resid 4 through 5 2281 hydrogen bonds defined for protein. 6411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2141 hydrogen bonds 3420 hydrogen bond angles 0 basepair planarities 890 basepair parallelities 1774 stacking parallelities Total time for adding SS restraints: 157.65 Time building geometry restraints manager: 48.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 13414 1.31 - 1.44: 53999 1.44 - 1.56: 58029 1.56 - 1.69: 6227 1.69 - 1.81: 246 Bond restraints: 131915 Sorted by residual: bond pdb=" CG LEU 3 112 " pdb=" CD2 LEU 3 112 " ideal model delta sigma weight residual 1.521 1.373 0.148 3.30e-02 9.18e+02 2.02e+01 bond pdb=" CD LYS u 38 " pdb=" CE LYS u 38 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.76e+00 bond pdb=" CB ARG u 23 " pdb=" CG ARG u 23 " ideal model delta sigma weight residual 1.520 1.434 0.086 3.00e-02 1.11e+03 8.31e+00 bond pdb=" CG ASN b 42 " pdb=" ND2 ASN b 42 " ideal model delta sigma weight residual 1.328 1.269 0.059 2.10e-02 2.27e+03 7.86e+00 bond pdb=" CA PHE m 645 " pdb=" C PHE m 645 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.02e-02 9.61e+03 7.22e+00 ... (remaining 131910 not shown) Histogram of bond angle deviations from ideal: 95.32 - 103.07: 6509 103.07 - 110.83: 64029 110.83 - 118.58: 52939 118.58 - 126.33: 59720 126.33 - 134.08: 10181 Bond angle restraints: 193378 Sorted by residual: angle pdb=" N LYS F 89 " pdb=" CA LYS F 89 " pdb=" C LYS F 89 " ideal model delta sigma weight residual 113.41 108.26 5.15 1.22e+00 6.72e-01 1.78e+01 angle pdb=" N GLN T 103 " pdb=" CA GLN T 103 " pdb=" C GLN T 103 " ideal model delta sigma weight residual 110.97 106.44 4.53 1.09e+00 8.42e-01 1.72e+01 angle pdb=" N HIS 3 13 " pdb=" CA HIS 3 13 " pdb=" C HIS 3 13 " ideal model delta sigma weight residual 110.80 118.95 -8.15 2.13e+00 2.20e-01 1.47e+01 angle pdb=" O3' G 11238 " pdb=" C3' G 11238 " pdb=" C2' G 11238 " ideal model delta sigma weight residual 109.50 114.86 -5.36 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C LEU m 643 " pdb=" N ASP m 644 " pdb=" CA ASP m 644 " ideal model delta sigma weight residual 122.65 116.94 5.71 1.60e+00 3.91e-01 1.27e+01 ... (remaining 193373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 74847 35.98 - 71.95: 7454 71.95 - 107.93: 794 107.93 - 143.91: 6 143.91 - 179.89: 26 Dihedral angle restraints: 83127 sinusoidal: 62429 harmonic: 20698 Sorted by residual: dihedral pdb=" O4' U 13407 " pdb=" C1' U 13407 " pdb=" N1 U 13407 " pdb=" C2 U 13407 " ideal model delta sinusoidal sigma weight residual 200.00 20.88 179.12 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual 200.00 26.86 173.14 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 12654 " pdb=" C1' U 12654 " pdb=" N1 U 12654 " pdb=" C2 U 12654 " ideal model delta sinusoidal sigma weight residual 200.00 38.23 161.77 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 83124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 23073 0.084 - 0.168: 948 0.168 - 0.252: 29 0.252 - 0.337: 1 0.337 - 0.421: 1 Chirality restraints: 24052 Sorted by residual: chirality pdb=" CG LEU 3 112 " pdb=" CB LEU 3 112 " pdb=" CD1 LEU 3 112 " pdb=" CD2 LEU 3 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA HIS 3 13 " pdb=" N HIS 3 13 " pdb=" C HIS 3 13 " pdb=" CB HIS 3 13 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' A 1 968 " pdb=" C4' A 1 968 " pdb=" O3' A 1 968 " pdb=" C2' A 1 968 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 24049 not shown) Planarity restraints: 12950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR m 689 " 0.034 2.00e-02 2.50e+03 2.86e-02 1.64e+01 pdb=" CG TYR m 689 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR m 689 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR m 689 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR m 689 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR m 689 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR m 689 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR m 689 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN b 42 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" CG ASN b 42 " -0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN b 42 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN b 42 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11913 " -0.043 2.00e-02 2.50e+03 1.80e-02 8.92e+00 pdb=" N9 A 11913 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A 11913 " 0.007 2.00e-02 2.50e+03 pdb=" N7 A 11913 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A 11913 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 11913 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 11913 " -0.015 2.00e-02 2.50e+03 pdb=" N1 A 11913 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A 11913 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 11913 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A 11913 " 0.007 2.00e-02 2.50e+03 ... (remaining 12947 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 7045 2.69 - 3.25: 109538 3.25 - 3.80: 235211 3.80 - 4.35: 325103 4.35 - 4.90: 447946 Nonbonded interactions: 1124843 Sorted by model distance: nonbonded pdb=" O2' C 1 243 " pdb=" O5' G 1 244 " model vdw 2.143 2.440 nonbonded pdb=" O2' C 12779 " pdb=" O5' G 12780 " model vdw 2.161 2.440 nonbonded pdb=" OP1 C 1 347 " pdb=" O2' G 11414 " model vdw 2.197 2.440 nonbonded pdb=" OP2 G 2 111 " pdb=" O2' A 2 113 " model vdw 2.197 2.440 nonbonded pdb=" OP1 G 1 343 " pdb=" OG1 THR Y 8 " model vdw 2.200 2.440 ... (remaining 1124838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 28.480 Check model and map are aligned: 1.340 Set scattering table: 0.820 Process input model: 389.880 Find NCS groups from input model: 2.720 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 430.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 131915 Z= 0.245 Angle : 0.518 9.931 193378 Z= 0.277 Chirality : 0.035 0.421 24052 Planarity : 0.004 0.069 12950 Dihedral : 21.913 179.887 69767 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 0.18 % Allowed : 6.47 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.10), residues: 7029 helix: 0.80 (0.11), residues: 2324 sheet: -0.28 (0.15), residues: 1216 loop : -0.38 (0.11), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 100 HIS 0.007 0.001 HIS P 145 PHE 0.041 0.001 PHE u 29 TYR 0.044 0.002 TYR m 689 ARG 0.050 0.001 ARG m 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 603 time to evaluate : 6.601 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: P 109 MET cc_start: 0.8043 (mmm) cc_final: 0.7724 (mmm) REVERT: X 99 ARG cc_start: 0.7690 (ttm170) cc_final: 0.7457 (mtm-85) REVERT: u 23 ARG cc_start: 0.7028 (mtp180) cc_final: 0.6514 (mtp180) outliers start: 10 outliers final: 5 residues processed: 606 average time/residue: 1.1328 time to fit residues: 1180.1768 Evaluate side-chains 592 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 587 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain m residue 644 ASP Chi-restraints excluded: chain o residue 65 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 847 optimal weight: 0.6980 chunk 760 optimal weight: 9.9990 chunk 422 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 513 optimal weight: 20.0000 chunk 406 optimal weight: 0.9990 chunk 786 optimal weight: 0.2980 chunk 304 optimal weight: 0.9980 chunk 478 optimal weight: 2.9990 chunk 585 optimal weight: 4.9990 chunk 911 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 3 GLN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 170 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** X 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 GLN a 66 ASN b 6 ASN b 47 ASN f 107 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 4 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 131915 Z= 0.134 Angle : 0.530 9.127 193378 Z= 0.276 Chirality : 0.035 0.211 24052 Planarity : 0.004 0.046 12950 Dihedral : 22.546 179.726 56155 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 0.83 % Allowed : 7.92 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.10), residues: 7029 helix: 1.38 (0.11), residues: 2327 sheet: -0.21 (0.15), residues: 1215 loop : -0.25 (0.11), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 100 HIS 0.005 0.001 HIS u 4 PHE 0.032 0.001 PHE O 48 TYR 0.018 0.001 TYR U 33 ARG 0.007 0.000 ARG N 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 629 time to evaluate : 6.324 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: C 101 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7819 (ptt) REVERT: I 162 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7421 (mm110) REVERT: N 104 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7426 (mm-30) REVERT: c 87 ASN cc_start: 0.8370 (p0) cc_final: 0.8122 (p0) outliers start: 47 outliers final: 35 residues processed: 651 average time/residue: 1.1009 time to fit residues: 1226.9317 Evaluate side-chains 633 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 597 time to evaluate : 6.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 83 SER Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 66 ASN Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 27 GLU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain n residue 187 ILE Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain u residue 13 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 506 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 758 optimal weight: 10.0000 chunk 620 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 913 optimal weight: 0.0170 chunk 986 optimal weight: 50.0000 chunk 813 optimal weight: 4.9990 chunk 905 optimal weight: 0.0870 chunk 311 optimal weight: 0.8980 chunk 732 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN F 135 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** X 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 43 GLN b 47 ASN g 103 GLN ** n 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 4 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 131915 Z= 0.281 Angle : 0.580 9.917 193378 Z= 0.299 Chirality : 0.039 0.246 24052 Planarity : 0.005 0.084 12950 Dihedral : 22.424 179.986 56147 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 1.46 % Allowed : 10.16 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7029 helix: 1.37 (0.11), residues: 2327 sheet: -0.24 (0.15), residues: 1214 loop : -0.31 (0.11), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP j 49 HIS 0.007 0.001 HIS b 7 PHE 0.020 0.002 PHE O 48 TYR 0.032 0.002 TYR U 33 ARG 0.005 0.001 ARG i 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 606 time to evaluate : 6.243 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: C 101 MET cc_start: 0.8603 (ptt) cc_final: 0.8401 (ptt) REVERT: F 153 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: L 172 ASN cc_start: 0.7762 (p0) cc_final: 0.7519 (p0) REVERT: N 104 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7705 (mt-10) outliers start: 83 outliers final: 63 residues processed: 654 average time/residue: 1.1084 time to fit residues: 1250.4520 Evaluate side-chains 647 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 583 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 91 ASN Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain e residue 27 GLU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 902 optimal weight: 30.0000 chunk 686 optimal weight: 4.9990 chunk 474 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 613 optimal weight: 1.9990 chunk 916 optimal weight: 10.0000 chunk 970 optimal weight: 5.9990 chunk 478 optimal weight: 1.9990 chunk 868 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN L 196 GLN N 91 HIS ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 47 ASN g 103 GLN u 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 131915 Z= 0.255 Angle : 0.555 11.472 193378 Z= 0.288 Chirality : 0.038 0.236 24052 Planarity : 0.004 0.067 12950 Dihedral : 22.398 179.934 56145 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 1.68 % Allowed : 11.66 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7029 helix: 1.41 (0.11), residues: 2319 sheet: -0.24 (0.15), residues: 1206 loop : -0.34 (0.11), residues: 3504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 108 HIS 0.006 0.001 HIS a 40 PHE 0.016 0.001 PHE d 44 TYR 0.024 0.001 TYR U 73 ARG 0.006 0.000 ARG i 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 602 time to evaluate : 6.268 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: F 153 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: L 172 ASN cc_start: 0.7765 (p0) cc_final: 0.7522 (p0) REVERT: N 104 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7607 (mt-10) REVERT: O 101 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: k 57 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7137 (tt) REVERT: o 16 ASN cc_start: 0.7305 (m110) cc_final: 0.7075 (m110) outliers start: 95 outliers final: 71 residues processed: 659 average time/residue: 1.0691 time to fit residues: 1216.6019 Evaluate side-chains 657 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 583 time to evaluate : 6.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 91 ASN Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain e residue 27 GLU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 808 optimal weight: 8.9990 chunk 550 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 722 optimal weight: 20.0000 chunk 400 optimal weight: 0.7980 chunk 828 optimal weight: 8.9990 chunk 670 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 495 optimal weight: 3.9990 chunk 871 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 47 ASN u 4 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 131915 Z= 0.290 Angle : 0.579 11.562 193378 Z= 0.298 Chirality : 0.039 0.239 24052 Planarity : 0.005 0.078 12950 Dihedral : 22.367 179.715 56145 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 2.08 % Allowed : 12.52 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 7029 helix: 1.39 (0.11), residues: 2319 sheet: -0.24 (0.15), residues: 1207 loop : -0.37 (0.11), residues: 3503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 162 HIS 0.006 0.001 HIS a 40 PHE 0.017 0.001 PHE d 44 TYR 0.021 0.002 TYR g 13 ARG 0.009 0.000 ARG i 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 596 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 101 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8239 (ptt) REVERT: F 153 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: F 247 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: G 109 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8191 (mp) REVERT: L 172 ASN cc_start: 0.7803 (p0) cc_final: 0.7550 (p0) REVERT: N 104 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7713 (mt-10) REVERT: O 101 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: P 147 GLU cc_start: 0.7389 (pt0) cc_final: 0.7140 (pt0) REVERT: U 37 ARG cc_start: 0.6375 (mtt180) cc_final: 0.6102 (mtt180) REVERT: f 61 ARG cc_start: 0.6659 (mpt180) cc_final: 0.6137 (mpt180) REVERT: k 57 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7260 (tt) REVERT: n 564 MET cc_start: 0.4216 (tmm) cc_final: 0.3883 (tmm) REVERT: o 16 ASN cc_start: 0.7328 (m110) cc_final: 0.7118 (m110) outliers start: 118 outliers final: 90 residues processed: 677 average time/residue: 1.1672 time to fit residues: 1375.2917 Evaluate side-chains 667 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 571 time to evaluate : 6.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain e residue 27 GLU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain k residue 2 PRO Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 326 optimal weight: 7.9990 chunk 873 optimal weight: 0.0970 chunk 191 optimal weight: 10.0000 chunk 569 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 971 optimal weight: 9.9990 chunk 806 optimal weight: 2.9990 chunk 449 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 509 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 193 ASN A 220 HIS B 163 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 ASN L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN b 6 ASN b 47 ASN b 56 GLN u 4 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 131915 Z= 0.422 Angle : 0.674 12.444 193378 Z= 0.343 Chirality : 0.044 0.302 24052 Planarity : 0.006 0.095 12950 Dihedral : 22.427 179.718 56145 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.45 % Allowed : 12.75 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.10), residues: 7029 helix: 1.22 (0.11), residues: 2315 sheet: -0.30 (0.15), residues: 1197 loop : -0.51 (0.10), residues: 3517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 162 HIS 0.010 0.002 HIS C 85 PHE 0.019 0.002 PHE O 48 TYR 0.025 0.002 TYR g 13 ARG 0.008 0.001 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 583 time to evaluate : 6.259 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: F 153 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: G 109 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8240 (mp) REVERT: O 101 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: P 147 GLU cc_start: 0.7473 (pt0) cc_final: 0.7237 (pt0) REVERT: U 37 ARG cc_start: 0.6422 (mtt180) cc_final: 0.6178 (mtt180) REVERT: Y 66 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: h 62 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6962 (mt-10) REVERT: k 57 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7243 (tt) REVERT: o 16 ASN cc_start: 0.7318 (m110) cc_final: 0.7101 (m110) REVERT: u 29 PHE cc_start: 0.7658 (m-80) cc_final: 0.7455 (m-80) REVERT: u 42 MET cc_start: 0.7047 (mtt) cc_final: 0.6516 (mtm) outliers start: 139 outliers final: 109 residues processed: 679 average time/residue: 1.1650 time to fit residues: 1375.9098 Evaluate side-chains 681 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 567 time to evaluate : 6.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 161 ASN Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 80 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 109 THR Chi-restraints excluded: chain e residue 27 GLU Chi-restraints excluded: chain g residue 22 ILE Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 32 VAL Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 2 PRO Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain m residue 639 CYS Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 25 ASP Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 936 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 553 optimal weight: 8.9990 chunk 709 optimal weight: 0.9980 chunk 549 optimal weight: 20.0000 chunk 817 optimal weight: 0.7980 chunk 542 optimal weight: 7.9990 chunk 967 optimal weight: 0.6980 chunk 605 optimal weight: 1.9990 chunk 589 optimal weight: 1.9990 chunk 446 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN A 27 GLN A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN L 196 GLN M 81 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 47 ASN b 56 GLN h 61 ASN u 4 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 131915 Z= 0.190 Angle : 0.548 13.980 193378 Z= 0.284 Chirality : 0.037 0.244 24052 Planarity : 0.004 0.051 12950 Dihedral : 22.432 179.579 56145 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 2.03 % Allowed : 13.60 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 7029 helix: 1.37 (0.11), residues: 2324 sheet: -0.30 (0.15), residues: 1191 loop : -0.43 (0.11), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 162 HIS 0.006 0.001 HIS E 191 PHE 0.023 0.001 PHE k 35 TYR 0.024 0.001 TYR U 73 ARG 0.010 0.000 ARG N 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 593 time to evaluate : 6.224 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: 8 28 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6903 (mtt180) REVERT: C 101 MET cc_start: 0.8342 (ptt) cc_final: 0.8059 (ptt) REVERT: F 153 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: F 247 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: O 101 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: P 147 GLU cc_start: 0.7333 (pt0) cc_final: 0.7094 (pt0) REVERT: f 61 ARG cc_start: 0.6241 (mpt180) cc_final: 0.5776 (mpt180) REVERT: k 57 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7170 (tt) REVERT: o 16 ASN cc_start: 0.7251 (m110) cc_final: 0.7040 (m110) REVERT: u 42 MET cc_start: 0.6944 (mtt) cc_final: 0.6454 (mtm) outliers start: 115 outliers final: 98 residues processed: 674 average time/residue: 1.0760 time to fit residues: 1257.0890 Evaluate side-chains 678 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 576 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 122 GLU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain k residue 68 THR Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 598 optimal weight: 10.0000 chunk 386 optimal weight: 7.9990 chunk 577 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 615 optimal weight: 0.6980 chunk 659 optimal weight: 0.0770 chunk 478 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 760 optimal weight: 7.9990 overall best weight: 2.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN A 27 GLN A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 ASN L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN b 56 GLN u 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 131915 Z= 0.254 Angle : 0.560 14.024 193378 Z= 0.290 Chirality : 0.037 0.302 24052 Planarity : 0.005 0.055 12950 Dihedral : 22.353 179.948 56145 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 2.24 % Allowed : 13.62 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 7029 helix: 1.38 (0.11), residues: 2325 sheet: -0.31 (0.15), residues: 1198 loop : -0.44 (0.11), residues: 3506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 162 HIS 0.006 0.001 HIS 3 71 PHE 0.019 0.001 PHE I 46 TYR 0.021 0.001 TYR 3 63 ARG 0.010 0.000 ARG N 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 578 time to evaluate : 6.257 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: F 153 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: F 247 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: O 101 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: P 147 GLU cc_start: 0.7348 (pt0) cc_final: 0.7117 (pt0) REVERT: Y 66 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: f 61 ARG cc_start: 0.6298 (mpt180) cc_final: 0.5987 (mpt180) REVERT: k 57 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7281 (tt) REVERT: o 16 ASN cc_start: 0.7352 (m110) cc_final: 0.7151 (m110) REVERT: u 42 MET cc_start: 0.6970 (mtt) cc_final: 0.6482 (mtm) outliers start: 127 outliers final: 107 residues processed: 668 average time/residue: 1.0906 time to fit residues: 1261.2613 Evaluate side-chains 681 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 569 time to evaluate : 6.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 25 GLN Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain L residue 172 ASN Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 130 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 7 HIS Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 14 THR Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain g residue 22 ILE Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 6 SER Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain m residue 639 CYS Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 201 ILE Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 880 optimal weight: 7.9990 chunk 927 optimal weight: 0.8980 chunk 845 optimal weight: 3.9990 chunk 901 optimal weight: 50.0000 chunk 926 optimal weight: 0.2980 chunk 542 optimal weight: 8.9990 chunk 392 optimal weight: 3.9990 chunk 708 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 814 optimal weight: 8.9990 chunk 852 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 GLN A 27 GLN A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN J 43 GLN L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 6 ASN b 56 GLN u 4 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 131915 Z= 0.284 Angle : 0.577 14.356 193378 Z= 0.298 Chirality : 0.038 0.307 24052 Planarity : 0.005 0.058 12950 Dihedral : 22.338 179.748 56145 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 2.20 % Allowed : 13.94 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.10), residues: 7029 helix: 1.37 (0.11), residues: 2323 sheet: -0.30 (0.15), residues: 1195 loop : -0.47 (0.11), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 162 HIS 0.007 0.001 HIS 3 71 PHE 0.017 0.001 PHE k 35 TYR 0.022 0.002 TYR 3 63 ARG 0.011 0.000 ARG m 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 571 time to evaluate : 6.245 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: 8 39 MET cc_start: 0.6700 (mmm) cc_final: 0.6336 (mmt) REVERT: F 153 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: F 247 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: O 3 GLU cc_start: 0.6567 (pp20) cc_final: 0.6347 (pp20) REVERT: O 101 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: P 147 GLU cc_start: 0.7423 (pt0) cc_final: 0.7223 (pt0) REVERT: S 89 MET cc_start: 0.7955 (mmt) cc_final: 0.7684 (mmt) REVERT: Y 66 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: k 57 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7378 (tt) outliers start: 125 outliers final: 109 residues processed: 665 average time/residue: 1.0737 time to fit residues: 1232.2028 Evaluate side-chains 679 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 565 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain Z residue 124 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain b residue 6 ASN Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 14 THR Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 76 LEU Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain g residue 22 ILE Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain m residue 639 CYS Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 201 ILE Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 898 optimal weight: 50.0000 chunk 592 optimal weight: 6.9990 chunk 953 optimal weight: 30.0000 chunk 582 optimal weight: 0.7980 chunk 452 optimal weight: 3.9990 chunk 662 optimal weight: 0.9990 chunk 1000 optimal weight: 0.6980 chunk 920 optimal weight: 0.0970 chunk 796 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 615 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 193 ASN A 220 HIS A 227 GLN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN L 196 GLN ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 ASN b 56 GLN u 4 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.109 131915 Z= 0.145 Angle : 0.518 15.182 193378 Z= 0.270 Chirality : 0.035 0.350 24052 Planarity : 0.004 0.050 12950 Dihedral : 22.355 179.806 56145 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 1.92 % Allowed : 14.52 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7029 helix: 1.49 (0.11), residues: 2326 sheet: -0.26 (0.15), residues: 1202 loop : -0.39 (0.11), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP 3 77 HIS 0.019 0.001 HIS b 7 PHE 0.042 0.001 PHE I 46 TYR 0.031 0.001 TYR 3 63 ARG 0.031 0.000 ARG I 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14058 Ramachandran restraints generated. 7029 Oldfield, 0 Emsley, 7029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 583 time to evaluate : 5.692 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: 8 39 MET cc_start: 0.6651 (mmm) cc_final: 0.6299 (mmt) REVERT: F 153 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 247 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: O 3 GLU cc_start: 0.6608 (pp20) cc_final: 0.6374 (pp20) REVERT: O 101 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: P 147 GLU cc_start: 0.7268 (pt0) cc_final: 0.7051 (pt0) REVERT: S 89 MET cc_start: 0.7922 (mmt) cc_final: 0.7644 (mmt) REVERT: Y 66 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: f 61 ARG cc_start: 0.6151 (mpt180) cc_final: 0.5708 (mpt180) REVERT: k 57 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7207 (tt) outliers start: 109 outliers final: 93 residues processed: 661 average time/residue: 1.0734 time to fit residues: 1226.9022 Evaluate side-chains 674 residues out of total 6076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 576 time to evaluate : 5.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 GLN Chi-restraints excluded: chain 3 residue 50 TYR Chi-restraints excluded: chain 3 residue 53 VAL Chi-restraints excluded: chain 3 residue 71 HIS Chi-restraints excluded: chain 8 residue 10 LYS Chi-restraints excluded: chain 8 residue 47 THR Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 140 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain L residue 156 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 101 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 130 LEU Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain R residue 59 SER Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 15 THR Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain T residue 89 VAL Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 95 SER Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 87 LEU Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 6 ASP Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Z residue 68 VAL Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 89 LEU Chi-restraints excluded: chain Z residue 105 THR Chi-restraints excluded: chain Z residue 108 SER Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 143 VAL Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 77 SER Chi-restraints excluded: chain d residue 14 THR Chi-restraints excluded: chain d residue 21 MET Chi-restraints excluded: chain d residue 97 GLN Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain h residue 48 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain j residue 64 MET Chi-restraints excluded: chain k residue 57 LEU Chi-restraints excluded: chain n residue 121 GLU Chi-restraints excluded: chain n residue 201 ILE Chi-restraints excluded: chain n residue 560 LEU Chi-restraints excluded: chain o residue 26 THR Chi-restraints excluded: chain o residue 34 SER Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 488 optimal weight: 3.9990 chunk 632 optimal weight: 2.9990 chunk 848 optimal weight: 0.1980 chunk 244 optimal weight: 10.0000 chunk 734 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 797 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 819 optimal weight: 0.0570 chunk 101 optimal weight: 10.0000 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 GLN A 193 ASN A 220 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 HIS b 47 ASN u 4 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.122991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.110129 restraints weight = 209343.498| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 0.46 r_work: 0.3333 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 131915 Z= 0.209 Angle : 0.532 15.507 193378 Z= 0.276 Chirality : 0.036 0.388 24052 Planarity : 0.004 0.085 12950 Dihedral : 22.275 179.377 56145 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.85 % Allowed : 14.64 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.10), residues: 7029 helix: 1.49 (0.11), residues: 2329 sheet: -0.23 (0.15), residues: 1202 loop : -0.39 (0.11), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 3 77 HIS 0.006 0.001 HIS E 191 PHE 0.048 0.001 PHE I 46 TYR 0.025 0.001 TYR 3 63 ARG 0.012 0.000 ARG m 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22290.08 seconds wall clock time: 395 minutes 21.68 seconds (23721.68 seconds total)