Starting phenix.real_space_refine on Thu Sep 26 09:00:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iai_35302/09_2024/8iai_35302.cif" } resolution = 3.5 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= 0.002 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 383 5.16 5 C 37998 2.51 5 N 10433 2.21 5 O 11464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 60300 Number of models: 1 Model: "" Number of chains: 42 Chain: "1" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2578 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain breaks: 2 Chain: "2" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2234 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain breaks: 1 Chain: "3" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2639 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2041 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Chain: "5" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 17, 'TRANS': 101} Chain breaks: 2 Chain: "6" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 17, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "7" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 17, 'TRANS': 98} Chain breaks: 2 Chain: "9" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 530 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "D" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "H" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "I" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2917 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "J" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2893 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "K" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2889 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "M" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1065 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1073 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "P" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1057 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "R" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "S" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1048 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "T" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1048 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "U" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2000 Classifications: {'peptide': 247} Link IDs: {'TRANS': 246} Chain: "V" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2011 Classifications: {'peptide': 246} Link IDs: {'TRANS': 245} Chain: "Y" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2119 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "Z" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 798 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.83, per 1000 atoms: 0.44 Number of scatterers: 60300 At special positions: 0 Unit cell: (128.78, 131.52, 439.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 383 16.00 P 22 15.00 O 11464 8.00 N 10433 7.00 C 37998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.01 Conformation dependent library (CDL) restraints added in 6.1 seconds 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14272 Finding SS restraints... Secondary structure from input PDB file: 348 helices and 72 sheets defined 55.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain '1' and resid 112 through 125 removed outlier: 3.530A pdb=" N ALA 1 116 " --> pdb=" O GLY 1 112 " (cutoff:3.500A) Processing helix chain '1' and resid 132 through 136 removed outlier: 3.545A pdb=" N SER 1 135 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE 1 136 " --> pdb=" O SER 1 133 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 132 through 136' Processing helix chain '1' and resid 139 through 159 Processing helix chain '1' and resid 188 through 192 removed outlier: 3.547A pdb=" N GLU 1 191 " --> pdb=" O LEU 1 188 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL 1 192 " --> pdb=" O TYR 1 189 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 188 through 192' Processing helix chain '1' and resid 217 through 231 removed outlier: 3.647A pdb=" N PHE 1 221 " --> pdb=" O ASN 1 217 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU 1 223 " --> pdb=" O ALA 1 219 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N HIS 1 224 " --> pdb=" O GLY 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 242 through 250 removed outlier: 3.569A pdb=" N ALA 1 246 " --> pdb=" O THR 1 242 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA 1 247 " --> pdb=" O PRO 1 243 " (cutoff:3.500A) Processing helix chain '1' and resid 259 through 266 removed outlier: 3.646A pdb=" N LEU 1 265 " --> pdb=" O GLU 1 261 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY 1 266 " --> pdb=" O ALA 1 262 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 3.747A pdb=" N VAL 1 284 " --> pdb=" O GLU 1 280 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY 1 291 " --> pdb=" O GLN 1 287 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 336 Processing helix chain '1' and resid 337 through 341 Processing helix chain '1' and resid 373 through 388 removed outlier: 3.722A pdb=" N PHE 1 377 " --> pdb=" O GLY 1 373 " (cutoff:3.500A) Processing helix chain '1' and resid 495 through 513 removed outlier: 4.471A pdb=" N VAL 1 499 " --> pdb=" O ASN 1 495 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN 1 500 " --> pdb=" O PRO 1 496 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN 1 510 " --> pdb=" O ILE 1 506 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 1 511 " --> pdb=" O ARG 1 507 " (cutoff:3.500A) Processing helix chain '2' and resid 112 through 125 Processing helix chain '2' and resid 139 through 160 removed outlier: 3.572A pdb=" N CYS 2 147 " --> pdb=" O LYS 2 143 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 2 148 " --> pdb=" O LEU 2 144 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP 2 157 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU 2 158 " --> pdb=" O ARG 2 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 2 159 " --> pdb=" O LEU 2 155 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY 2 160 " --> pdb=" O ALA 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 192 removed outlier: 3.602A pdb=" N GLU 2 191 " --> pdb=" O LEU 2 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL 2 192 " --> pdb=" O TYR 2 189 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 188 through 192' Processing helix chain '2' and resid 217 through 231 removed outlier: 3.630A pdb=" N PHE 2 221 " --> pdb=" O ASN 2 217 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU 2 223 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS 2 224 " --> pdb=" O GLY 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 250 Processing helix chain '2' and resid 259 through 266 removed outlier: 3.540A pdb=" N LEU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY 2 266 " --> pdb=" O ALA 2 262 " (cutoff:3.500A) Processing helix chain '2' and resid 278 through 290 removed outlier: 3.931A pdb=" N GLU 2 282 " --> pdb=" O VAL 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 335 removed outlier: 3.691A pdb=" N ARG 2 330 " --> pdb=" O GLU 2 326 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER 2 334 " --> pdb=" O ARG 2 330 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA 2 335 " --> pdb=" O THR 2 331 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 354 Processing helix chain '2' and resid 373 through 388 removed outlier: 3.674A pdb=" N PHE 2 377 " --> pdb=" O GLY 2 373 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 122 Processing helix chain '3' and resid 129 through 147 removed outlier: 4.133A pdb=" N CYS 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 3 140 " --> pdb=" O LYS 3 136 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 3 141 " --> pdb=" O ILE 3 137 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 180 removed outlier: 3.566A pdb=" N VAL 3 180 " --> pdb=" O CYS 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 208 through 217 removed outlier: 4.412A pdb=" N HIS 3 212 " --> pdb=" O GLY 3 208 " (cutoff:3.500A) Processing helix chain '3' and resid 230 through 239 Processing helix chain '3' and resid 247 through 254 removed outlier: 3.797A pdb=" N GLY 3 254 " --> pdb=" O ALA 3 250 " (cutoff:3.500A) Processing helix chain '3' and resid 267 through 279 removed outlier: 3.541A pdb=" N ARG 3 271 " --> pdb=" O GLN 3 267 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY 3 279 " --> pdb=" O GLN 3 275 " (cutoff:3.500A) Processing helix chain '3' and resid 298 through 323 Processing helix chain '3' and resid 326 through 330 removed outlier: 3.720A pdb=" N ILE 3 330 " --> pdb=" O GLU 3 327 " (cutoff:3.500A) Processing helix chain '3' and resid 333 through 338 removed outlier: 4.654A pdb=" N HIS 3 337 " --> pdb=" O GLU 3 333 " (cutoff:3.500A) Processing helix chain '3' and resid 361 through 376 removed outlier: 3.883A pdb=" N ALA 3 367 " --> pdb=" O HIS 3 363 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 3 368 " --> pdb=" O GLU 3 364 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU 3 375 " --> pdb=" O MET 3 371 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY 3 376 " --> pdb=" O LEU 3 372 " (cutoff:3.500A) Processing helix chain '3' and resid 491 through 509 Processing helix chain '3' and resid 517 through 524 removed outlier: 3.659A pdb=" N VAL 3 523 " --> pdb=" O LEU 3 519 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE 3 524 " --> pdb=" O LEU 3 520 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 122 removed outlier: 3.893A pdb=" N ALA 4 121 " --> pdb=" O ASP 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 147 removed outlier: 4.569A pdb=" N CYS 4 135 " --> pdb=" O ARG 4 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS 4 136 " --> pdb=" O LEU 4 132 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 180 removed outlier: 3.755A pdb=" N VAL 4 180 " --> pdb=" O CYS 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 209 through 219 Processing helix chain '4' and resid 230 through 239 Processing helix chain '4' and resid 247 through 254 removed outlier: 3.797A pdb=" N GLY 4 254 " --> pdb=" O ALA 4 250 " (cutoff:3.500A) Processing helix chain '4' and resid 267 through 279 Processing helix chain '4' and resid 298 through 324 Processing helix chain '4' and resid 361 through 376 removed outlier: 4.076A pdb=" N PHE 4 365 " --> pdb=" O GLY 4 361 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 45 Processing helix chain '5' and resid 51 through 56 removed outlier: 4.132A pdb=" N ASP 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 5 56 " --> pdb=" O ALA 5 52 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 51 through 56' Processing helix chain '5' and resid 162 through 171 removed outlier: 3.521A pdb=" N LEU 5 166 " --> pdb=" O LEU 5 162 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE 5 167 " --> pdb=" O ILE 5 163 " (cutoff:3.500A) Processing helix chain '5' and resid 197 through 213 removed outlier: 3.542A pdb=" N VAL 5 201 " --> pdb=" O SER 5 197 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 45 Processing helix chain '6' and resid 162 through 171 removed outlier: 3.958A pdb=" N LEU 6 166 " --> pdb=" O LEU 6 162 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE 6 167 " --> pdb=" O ILE 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 197 through 213 Processing helix chain '7' and resid 40 through 45 Processing helix chain '7' and resid 51 through 56 removed outlier: 3.901A pdb=" N ASP 7 55 " --> pdb=" O LYS 7 51 " (cutoff:3.500A) Processing helix chain '7' and resid 145 through 149 Processing helix chain '7' and resid 161 through 171 Processing helix chain '7' and resid 197 through 213 Processing helix chain '9' and resid 23 through 27 Processing helix chain '9' and resid 32 through 40 removed outlier: 5.044A pdb=" N GLU 9 38 " --> pdb=" O GLU 9 34 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG 9 39 " --> pdb=" O TYR 9 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN 9 40 " --> pdb=" O LEU 9 36 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 56 removed outlier: 3.549A pdb=" N PHE 9 49 " --> pdb=" O LEU 9 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN 9 50 " --> pdb=" O ARG 9 46 " (cutoff:3.500A) Processing helix chain '9' and resid 56 through 64 Processing helix chain '9' and resid 64 through 82 removed outlier: 4.071A pdb=" N GLU 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS 9 81 " --> pdb=" O GLU 9 77 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY 9 82 " --> pdb=" O GLN 9 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 4.023A pdb=" N GLY A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.881A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.556A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.790A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.514A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.937A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.615A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.555A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.988A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.775A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.926A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.154A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.235A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.583A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.913A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.704A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.643A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 257 removed outlier: 3.540A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.159A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.573A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.001A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.758A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.160A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.703A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.705A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.772A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.653A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.935A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.095A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 252 through 260' Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.620A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.750A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.505A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.342A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.632A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.624A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.868A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.527A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.937A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 254 removed outlier: 3.984A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.748A pdb=" N GLU D 259 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.505A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.593A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.956A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.616A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.601A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.525A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.976A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.516A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.527A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 251 through 255 removed outlier: 3.912A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.799A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.099A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.934A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.847A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.565A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.647A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 216 removed outlier: 3.787A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 251 through 257 removed outlier: 3.644A pdb=" N ARG F 254 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 4.082A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.033A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.775A pdb=" N GLY F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.617A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.420A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.550A pdb=" N LYS G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.715A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.667A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 126 removed outlier: 3.809A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.560A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 202 through 216 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 251 through 256 removed outlier: 3.863A pdb=" N ARG G 254 " --> pdb=" O GLY G 251 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.007A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.775A pdb=" N GLY G 343 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.585A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.362A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 removed outlier: 3.712A pdb=" N MET H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.025A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.565A pdb=" N GLY H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 removed outlier: 3.533A pdb=" N ILE H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 172 through 175' Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.148A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 251 through 257 removed outlier: 3.665A pdb=" N ARG H 254 " --> pdb=" O GLY H 251 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 removed outlier: 4.133A pdb=" N PHE H 262 " --> pdb=" O PRO H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 289 through 296 removed outlier: 3.599A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 306 removed outlier: 4.235A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 350 through 355 Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 374 removed outlier: 4.369A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 removed outlier: 3.905A pdb=" N LYS I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 91 removed outlier: 3.754A pdb=" N MET I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.948A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.538A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 202 through 216 removed outlier: 4.009A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 251 through 256 removed outlier: 3.870A pdb=" N ARG I 254 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE I 255 " --> pdb=" O ASN I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 262 removed outlier: 3.524A pdb=" N ALA I 260 " --> pdb=" O CYS I 257 " (cutoff:3.500A) Processing helix chain 'I' and resid 263 through 268 removed outlier: 3.500A pdb=" N PHE I 266 " --> pdb=" O GLN I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 289 through 296 Processing helix chain 'I' and resid 301 through 306 removed outlier: 3.505A pdb=" N THR I 304 " --> pdb=" O GLY I 301 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 350 through 355 removed outlier: 3.513A pdb=" N GLN I 353 " --> pdb=" O SER I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 368 through 373 removed outlier: 4.189A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.020A pdb=" N LYS J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 92 removed outlier: 3.518A pdb=" N MET J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.529A pdb=" N HIS J 101 " --> pdb=" O PRO J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.928A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 146 removed outlier: 3.505A pdb=" N LEU J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 197 removed outlier: 4.075A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY J 197 " --> pdb=" O LEU J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 216 Processing helix chain 'J' and resid 222 through 233 removed outlier: 3.626A pdb=" N GLU J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 257 removed outlier: 3.688A pdb=" N ARG J 254 " --> pdb=" O GLY J 251 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE J 255 " --> pdb=" O ASN J 252 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS J 257 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 removed outlier: 4.260A pdb=" N PHE J 262 " --> pdb=" O PRO J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'J' and resid 301 through 306 removed outlier: 3.535A pdb=" N THR J 304 " --> pdb=" O GLY J 301 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 356 removed outlier: 3.523A pdb=" N GLN J 353 " --> pdb=" O SER J 350 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN J 354 " --> pdb=" O THR J 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP J 356 " --> pdb=" O GLN J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 374 removed outlier: 4.161A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.504A pdb=" N GLN K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER K 60 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 55 through 61' Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.559A pdb=" N MET K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 126 removed outlier: 3.830A pdb=" N GLU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 181 through 195 removed outlier: 4.157A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 216 Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 251 through 256 removed outlier: 3.956A pdb=" N ARG K 254 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE K 255 " --> pdb=" O ASN K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 262 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 296 removed outlier: 3.543A pdb=" N ARG K 290 " --> pdb=" O ASP K 286 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 3.855A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 removed outlier: 3.515A pdb=" N LEU K 320 " --> pdb=" O GLU K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 358 through 366 removed outlier: 3.680A pdb=" N ASP K 363 " --> pdb=" O LYS K 359 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 374 removed outlier: 3.531A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 68 removed outlier: 4.545A pdb=" N ILE M 45 " --> pdb=" O GLU M 41 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS M 46 " --> pdb=" O ARG M 42 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS M 62 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.706A pdb=" N LEU M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 97 Processing helix chain 'M' and resid 108 through 126 removed outlier: 3.541A pdb=" N ALA M 119 " --> pdb=" O ASN M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 140 Processing helix chain 'M' and resid 142 through 157 removed outlier: 3.546A pdb=" N PHE M 157 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 68 removed outlier: 4.080A pdb=" N VAL N 55 " --> pdb=" O GLU N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 82 Processing helix chain 'N' and resid 85 through 96 Processing helix chain 'N' and resid 108 through 126 removed outlier: 3.588A pdb=" N ALA N 119 " --> pdb=" O ASN N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 141 Processing helix chain 'N' and resid 142 through 157 Processing helix chain 'O' and resid 32 through 68 removed outlier: 4.091A pdb=" N LYS O 46 " --> pdb=" O ARG O 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS O 67 " --> pdb=" O TRP O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.898A pdb=" N LEU O 82 " --> pdb=" O LEU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 97 Processing helix chain 'O' and resid 108 through 126 removed outlier: 3.571A pdb=" N CYS O 112 " --> pdb=" O MET O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 141 Processing helix chain 'O' and resid 142 through 156 Processing helix chain 'P' and resid 43 through 69 removed outlier: 3.950A pdb=" N VAL P 55 " --> pdb=" O GLU P 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS P 58 " --> pdb=" O VAL P 54 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS P 67 " --> pdb=" O TRP P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 97 Processing helix chain 'P' and resid 108 through 126 removed outlier: 3.567A pdb=" N ALA P 119 " --> pdb=" O ASN P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 140 Processing helix chain 'P' and resid 142 through 158 Processing helix chain 'Q' and resid 33 through 69 removed outlier: 4.022A pdb=" N LYS Q 46 " --> pdb=" O ARG Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 3.701A pdb=" N LEU Q 82 " --> pdb=" O LEU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 97 Processing helix chain 'Q' and resid 108 through 126 removed outlier: 3.570A pdb=" N ALA Q 119 " --> pdb=" O ASN Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 140 removed outlier: 3.649A pdb=" N ILE Q 138 " --> pdb=" O GLY Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 157 removed outlier: 3.526A pdb=" N PHE Q 157 " --> pdb=" O ILE Q 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 68 removed outlier: 3.816A pdb=" N ALA R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.686A pdb=" N LEU R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 97 Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.591A pdb=" N GLN R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 140 Processing helix chain 'R' and resid 142 through 157 Processing helix chain 'S' and resid 32 through 69 removed outlier: 4.540A pdb=" N ILE S 45 " --> pdb=" O GLU S 41 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS S 67 " --> pdb=" O TRP S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 82 removed outlier: 3.747A pdb=" N LEU S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 97 Processing helix chain 'S' and resid 108 through 126 removed outlier: 3.568A pdb=" N ALA S 119 " --> pdb=" O ASN S 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN S 126 " --> pdb=" O PHE S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 134 through 141 Processing helix chain 'S' and resid 142 through 158 Processing helix chain 'T' and resid 32 through 69 removed outlier: 3.797A pdb=" N ILE T 45 " --> pdb=" O GLU T 41 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG T 52 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS T 58 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS T 67 " --> pdb=" O TRP T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.573A pdb=" N LEU T 82 " --> pdb=" O LEU T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 97 removed outlier: 3.669A pdb=" N GLY T 97 " --> pdb=" O GLU T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 126 removed outlier: 3.637A pdb=" N GLN T 126 " --> pdb=" O PHE T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 141 Processing helix chain 'T' and resid 142 through 158 removed outlier: 3.618A pdb=" N GLN T 158 " --> pdb=" O ILE T 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 248 removed outlier: 3.531A pdb=" N GLU U 8 " --> pdb=" O SER U 4 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA U 21 " --> pdb=" O LEU U 17 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR U 30 " --> pdb=" O GLU U 26 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN U 57 " --> pdb=" O ASN U 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE U 94 " --> pdb=" O GLY U 90 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL U 129 " --> pdb=" O LYS U 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA U 130 " --> pdb=" O TYR U 126 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG U 131 " --> pdb=" O GLU U 127 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA U 170 " --> pdb=" O GLN U 166 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU U 171 " --> pdb=" O THR U 167 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS U 184 " --> pdb=" O GLN U 180 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR U 185 " --> pdb=" O LYS U 181 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL U 191 " --> pdb=" O GLU U 187 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP U 218 " --> pdb=" O GLU U 214 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET U 248 " --> pdb=" O GLU U 244 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 246 removed outlier: 4.252A pdb=" N GLU V 48 " --> pdb=" O GLN V 44 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU V 88 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU V 103 " --> pdb=" O LEU V 99 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU V 120 " --> pdb=" O LYS V 116 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR V 126 " --> pdb=" O ALA V 122 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE V 135 " --> pdb=" O ARG V 131 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU V 156 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS V 177 " --> pdb=" O ALA V 173 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER V 179 " --> pdb=" O GLU V 175 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLN V 180 " --> pdb=" O GLU V 176 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE V 189 " --> pdb=" O TYR V 185 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG V 202 " --> pdb=" O GLU V 198 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA V 203 " --> pdb=" O ALA V 199 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS V 215 " --> pdb=" O ALA V 211 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR V 216 " --> pdb=" O LYS V 212 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR V 234 " --> pdb=" O GLU V 230 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 22 Processing helix chain 'Y' and resid 23 through 37 Processing helix chain 'Y' and resid 63 through 77 removed outlier: 3.959A pdb=" N LEU Y 67 " --> pdb=" O LYS Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 182 through 192 Processing helix chain 'Y' and resid 209 through 220 Processing helix chain 'Y' and resid 237 through 251 removed outlier: 3.951A pdb=" N LYS Y 249 " --> pdb=" O ALA Y 245 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL Y 250 " --> pdb=" O GLU Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 265 through 275 removed outlier: 3.624A pdb=" N ALA Y 275 " --> pdb=" O ARG Y 271 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 309 removed outlier: 3.555A pdb=" N ASN Y 309 " --> pdb=" O MET Y 305 " (cutoff:3.500A) Processing helix chain 'Y' and resid 321 through 349 Processing helix chain 'Z' and resid 13 through 30 removed outlier: 3.692A pdb=" N LYS Z 17 " --> pdb=" O PHE Z 13 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN Z 30 " --> pdb=" O PHE Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 53 removed outlier: 3.667A pdb=" N ARG Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE Z 53 " --> pdb=" O MET Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 89 Processing helix chain 'Z' and resid 90 through 96 Processing sheet with id=AA1, first strand: chain '1' and resid 206 through 208 removed outlier: 6.450A pdb=" N VAL 1 206 " --> pdb=" O ASN 1 201 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN 1 201 " --> pdb=" O VAL 1 206 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS 1 199 " --> pdb=" O ASP 1 208 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR 1 171 " --> pdb=" O LEU 1 181 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY 1 303 " --> pdb=" O LEU 1 299 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA 1 269 " --> pdb=" O ILE 1 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 198 through 200 removed outlier: 3.522A pdb=" N THR 2 171 " --> pdb=" O LEU 2 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 194 through 196 removed outlier: 3.605A pdb=" N GLU 3 196 " --> pdb=" O LYS 3 187 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL 3 292 " --> pdb=" O LEU 3 228 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA 3 257 " --> pdb=" O VAL 3 286 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ARG 3 288 " --> pdb=" O ALA 3 257 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE 3 259 " --> pdb=" O ARG 3 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 194 through 196 removed outlier: 7.315A pdb=" N LYS 4 187 " --> pdb=" O VAL 4 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 4 158 " --> pdb=" O ILE 4 225 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE 4 225 " --> pdb=" O THR 4 158 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU 4 228 " --> pdb=" O VAL 4 292 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL 4 292 " --> pdb=" O LEU 4 228 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.685A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ALA A 135 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.559A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.861A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 239 through 242 removed outlier: 4.067A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.587A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.601A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.683A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.522A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC2, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.294A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.762A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.976A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.651A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.471A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.005A pdb=" N THR E 106 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.513A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 176 through 178 removed outlier: 3.758A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 239 through 241 Processing sheet with id=AD8, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.009A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.456A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 176 through 178 removed outlier: 3.505A pdb=" N ALA F 170 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN H 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 239 through 241 Processing sheet with id=AE5, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.770A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA G 135 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AE7, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE8, first strand: chain 'G' and resid 176 through 178 removed outlier: 6.467A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 176 through 178 Processing sheet with id=AF1, first strand: chain 'G' and resid 239 through 241 Processing sheet with id=AF2, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.996A pdb=" N THR H 106 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN H 12 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET H 132 " --> pdb=" O ILE H 357 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AF4, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF5, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF6, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.416A pdb=" N ILE H 151 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER H 300 " --> pdb=" O ILE H 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET H 153 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 239 through 241 Processing sheet with id=AF8, first strand: chain 'I' and resid 29 through 32 removed outlier: 3.863A pdb=" N THR I 106 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN I 12 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET I 132 " --> pdb=" O ILE I 357 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE I 357 " --> pdb=" O MET I 132 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AG1, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AG2, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AG3, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.433A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 239 through 241 Processing sheet with id=AG5, first strand: chain 'J' and resid 29 through 32 removed outlier: 4.082A pdb=" N THR J 106 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN J 12 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA J 135 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET J 132 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.771A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AG8, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AG9, first strand: chain 'J' and resid 169 through 170 removed outlier: 6.644A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER J 300 " --> pdb=" O ILE J 151 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET J 153 " --> pdb=" O SER J 300 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 239 through 241 Processing sheet with id=AH2, first strand: chain 'K' and resid 29 through 31 removed outlier: 6.573A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR K 133 " --> pdb=" O VAL K 103 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AH4, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AH5, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AH6, first strand: chain 'K' and resid 169 through 170 removed outlier: 7.048A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N MET K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 239 through 241 Processing sheet with id=AH8, first strand: chain 'Y' and resid 199 through 201 removed outlier: 6.999A pdb=" N PHE Y 229 " --> pdb=" O ASN Y 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS Y 286 " --> pdb=" O LEU Y 257 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU Y 285 " --> pdb=" O GLY Y 316 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.557A pdb=" N GLN Z 68 " --> pdb=" O PHE Z 6 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE Z 69 " --> pdb=" O CYS Z 76 " (cutoff:3.500A) 3084 hydrogen bonds defined for protein. 8553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.38 Time building geometry restraints manager: 13.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15032 1.33 - 1.45: 11849 1.45 - 1.58: 33917 1.58 - 1.70: 34 1.70 - 1.82: 650 Bond restraints: 61482 Sorted by residual: bond pdb=" CG1 ILE Y 302 " pdb=" CD1 ILE Y 302 " ideal model delta sigma weight residual 1.513 1.407 0.106 3.90e-02 6.57e+02 7.32e+00 bond pdb=" C PRO Z 66 " pdb=" N PRO Z 67 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 bond pdb=" CG MET 4 371 " pdb=" SD MET 4 371 " ideal model delta sigma weight residual 1.803 1.755 0.048 2.50e-02 1.60e+03 3.68e+00 bond pdb=" C ALA V 174 " pdb=" O ALA V 174 " ideal model delta sigma weight residual 1.237 1.256 -0.020 1.19e-02 7.06e+03 2.72e+00 bond pdb=" C GLU U 128 " pdb=" O GLU U 128 " ideal model delta sigma weight residual 1.237 1.256 -0.019 1.19e-02 7.06e+03 2.52e+00 ... (remaining 61477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 82348 3.17 - 6.34: 707 6.34 - 9.52: 77 9.52 - 12.69: 17 12.69 - 15.86: 1 Bond angle restraints: 83150 Sorted by residual: angle pdb=" CA GLU P 53 " pdb=" CB GLU P 53 " pdb=" CG GLU P 53 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CA GLU T 53 " pdb=" CB GLU T 53 " pdb=" CG GLU T 53 " ideal model delta sigma weight residual 114.10 124.28 -10.18 2.00e+00 2.50e-01 2.59e+01 angle pdb=" CA GLN V 15 " pdb=" CB GLN V 15 " pdb=" CG GLN V 15 " ideal model delta sigma weight residual 114.10 123.84 -9.74 2.00e+00 2.50e-01 2.37e+01 angle pdb=" N GLU T 53 " pdb=" CA GLU T 53 " pdb=" CB GLU T 53 " ideal model delta sigma weight residual 110.28 117.79 -7.51 1.55e+00 4.16e-01 2.35e+01 angle pdb=" CA ARG 6 135 " pdb=" CB ARG 6 135 " pdb=" CG ARG 6 135 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 83145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.24: 34124 18.24 - 36.48: 2912 36.48 - 54.72: 403 54.72 - 72.96: 77 72.96 - 91.21: 42 Dihedral angle restraints: 37558 sinusoidal: 15461 harmonic: 22097 Sorted by residual: dihedral pdb=" CA LYS 1 348 " pdb=" C LYS 1 348 " pdb=" N TYR 1 349 " pdb=" CA TYR 1 349 " ideal model delta harmonic sigma weight residual 180.00 150.34 29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA LEU 4 132 " pdb=" C LEU 4 132 " pdb=" N MET 4 133 " pdb=" CA MET 4 133 " ideal model delta harmonic sigma weight residual -180.00 -153.14 -26.86 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -151.21 91.21 1 2.00e+01 2.50e-03 2.45e+01 ... (remaining 37555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 7758 0.060 - 0.120: 1377 0.120 - 0.180: 134 0.180 - 0.240: 14 0.240 - 0.300: 7 Chirality restraints: 9290 Sorted by residual: chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE H 250 " pdb=" CA ILE H 250 " pdb=" CG1 ILE H 250 " pdb=" CG2 ILE H 250 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA GLU T 53 " pdb=" N GLU T 53 " pdb=" C GLU T 53 " pdb=" CB GLU T 53 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 9287 not shown) Planarity restraints: 10688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 6 58 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.87e+00 pdb=" N PRO 6 59 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO 6 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 6 59 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO C 112 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO B 112 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.036 5.00e-02 4.00e+02 ... (remaining 10685 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1196 2.71 - 3.26: 57556 3.26 - 3.81: 92809 3.81 - 4.35: 116911 4.35 - 4.90: 199904 Nonbonded interactions: 468376 Sorted by model distance: nonbonded pdb=" OG1 THR G 202 " pdb=" OE1 GLU G 205 " model vdw 2.163 3.040 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 205 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR E 202 " pdb=" OE1 GLU E 205 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP 3 373 " pdb=" OH TYR 3 383 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR H 202 " pdb=" OE1 GLU H 205 " model vdw 2.211 3.040 ... (remaining 468371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 103 through 352 or resid 368 through 405)) selection = (chain '2' and (resid 103 through 352 or resid 368 through 405)) } ncs_group { reference = (chain '5' and (resid 39 through 66 or resid 118 through 150 or resid 160 throug \ h 201 or (resid 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 204 or (resid 205 through 213 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain '6' and (resid 39 through 66 or resid 118 through 213)) selection = (chain '7' and (resid 39 through 150 or resid 160 through 201 or (resid 202 and \ (name N or name CA or name C or name O or name CB )) or resid 203 through 204 or \ (resid 205 through 213 and (name N or name CA or name C or name O or name CB )) \ )) } ncs_group { reference = (chain 'A' and (resid 5 through 374 or resid 401)) selection = (chain 'B' and (resid 5 through 374 or resid 401)) selection = (chain 'C' and (resid 5 through 374 or resid 401)) selection = (chain 'D' and (resid 5 through 374 or resid 401)) selection = (chain 'E' and (resid 5 through 374 or resid 401)) selection = (chain 'F' and (resid 5 through 374 or resid 401)) selection = (chain 'G' and (resid 5 through 374 or resid 401)) selection = (chain 'H' and (resid 5 through 374 or resid 401)) selection = (chain 'I' and (resid 5 through 374 or resid 401)) selection = (chain 'J' and (resid 5 through 374 or resid 401)) selection = (chain 'K' and (resid 5 through 374 or resid 401)) } ncs_group { reference = (chain 'M' and resid 42 through 158) selection = chain 'N' selection = (chain 'O' and resid 42 through 158) selection = chain 'P' selection = (chain 'Q' and resid 42 through 158) selection = chain 'R' selection = (chain 'S' and resid 42 through 158) selection = (chain 'T' and resid 42 through 158) } 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 group one per residue 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: 9.860 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: 0.100 Extract box with map and model: 1.750 Check model and map are aligned: 0.390 Set scattering table: 0.510 Process input model: 113.330 Find NCS groups from input model: 2.930 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: 0.030 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.003 0.106 61482 Z= 0.226 Angle : 0.751 15.859 83150 Z= 0.394 Chirality : 0.046 0.300 9290 Planarity : 0.005 0.070 10688 Dihedral : 13.694 91.205 23286 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 7524 helix: 0.53 (0.08), residues: 3540 sheet: 0.39 (0.18), residues: 831 loop : -0.13 (0.11), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 151 HIS 0.008 0.001 HIS K 161 PHE 0.022 0.001 PHE 9 67 TYR 0.021 0.001 TYR 7 64 ARG 0.012 0.000 ARG N 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 789 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 302 HIS cc_start: 0.5755 (t-90) cc_final: 0.5436 (t-170) REVERT: 2 123 MET cc_start: 0.3514 (mmp) cc_final: 0.3208 (mmp) REVERT: 3 111 MET cc_start: 0.5606 (mmt) cc_final: 0.4631 (mtm) REVERT: 3 157 VAL cc_start: 0.7973 (t) cc_final: 0.6623 (t) REVERT: 4 377 TYR cc_start: 0.5783 (m-80) cc_final: 0.5361 (m-80) REVERT: 5 41 TYR cc_start: 0.7279 (t80) cc_final: 0.6825 (t80) REVERT: 6 130 HIS cc_start: 0.7481 (p-80) cc_final: 0.7276 (p-80) REVERT: 6 164 GLU cc_start: 0.7844 (mp0) cc_final: 0.7637 (mp0) REVERT: 7 39 LEU cc_start: 0.7865 (mt) cc_final: 0.7657 (mt) REVERT: 7 187 ILE cc_start: 0.8360 (mm) cc_final: 0.8073 (mt) REVERT: 7 192 TRP cc_start: 0.7729 (t-100) cc_final: 0.7520 (t-100) REVERT: 9 36 LEU cc_start: 0.7152 (tp) cc_final: 0.6515 (tp) REVERT: 9 37 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7749 (ptp-110) REVERT: 9 53 GLU cc_start: 0.8475 (pt0) cc_final: 0.7840 (tm-30) REVERT: 9 75 ILE cc_start: 0.9281 (mm) cc_final: 0.9063 (tp) REVERT: 9 80 LYS cc_start: 0.8295 (tppt) cc_final: 0.8085 (ttmt) REVERT: B 47 MET cc_start: 0.7937 (ttm) cc_final: 0.7605 (ttp) REVERT: D 167 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7836 (mm-30) REVERT: J 153 MET cc_start: 0.7861 (tmm) cc_final: 0.7644 (tmm) REVERT: J 355 MET cc_start: 0.7351 (tpp) cc_final: 0.7005 (tpp) REVERT: N 81 ASP cc_start: 0.7785 (m-30) cc_final: 0.7482 (m-30) REVERT: N 101 PRO cc_start: 0.8219 (Cg_exo) cc_final: 0.7909 (Cg_endo) REVERT: Q 61 THR cc_start: 0.8636 (m) cc_final: 0.8318 (m) REVERT: R 117 ASP cc_start: 0.7974 (t70) cc_final: 0.7709 (t0) REVERT: S 31 ASP cc_start: 0.5890 (t0) cc_final: 0.5431 (t70) REVERT: U 37 TYR cc_start: 0.8861 (t80) cc_final: 0.8567 (t80) REVERT: U 172 MET cc_start: 0.8869 (mmp) cc_final: 0.8498 (mmt) REVERT: V 152 SER cc_start: 0.8330 (t) cc_final: 0.8057 (p) REVERT: Z 3 ILE cc_start: 0.6931 (mm) cc_final: 0.6519 (mm) REVERT: Z 21 GLN cc_start: 0.7650 (mt0) cc_final: 0.7137 (mt0) REVERT: Z 48 TRP cc_start: 0.8029 (t60) cc_final: 0.7786 (t60) REVERT: Z 50 TYR cc_start: 0.7508 (m-80) cc_final: 0.7001 (m-80) REVERT: Z 84 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8074 (mm-30) outliers start: 0 outliers final: 0 residues processed: 789 average time/residue: 0.5509 time to fit residues: 751.7730 Evaluate side-chains 602 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 629 optimal weight: 2.9990 chunk 565 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 193 optimal weight: 0.0370 chunk 381 optimal weight: 0.6980 chunk 302 optimal weight: 3.9990 chunk 584 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 355 optimal weight: 5.9990 chunk 435 optimal weight: 0.8980 chunk 677 optimal weight: 9.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 227 HIS ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN K 12 ASN ** K 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 129 HIS T 34 ASN T 65 ASN U 117 HIS Z 21 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61482 Z= 0.164 Angle : 0.565 10.150 83150 Z= 0.284 Chirality : 0.041 0.280 9290 Planarity : 0.004 0.051 10688 Dihedral : 5.809 84.405 8390 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.69 % Allowed : 5.75 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 7524 helix: 1.29 (0.09), residues: 3620 sheet: 0.34 (0.17), residues: 877 loop : 0.19 (0.12), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 4 241 HIS 0.006 0.001 HIS 4 212 PHE 0.022 0.001 PHE B 279 TYR 0.022 0.001 TYR Z 75 ARG 0.008 0.000 ARG 9 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 647 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 302 HIS cc_start: 0.5632 (t-90) cc_final: 0.5392 (t-170) REVERT: 2 251 MET cc_start: 0.1973 (tpt) cc_final: -0.0093 (ptm) REVERT: 3 111 MET cc_start: 0.5434 (mmt) cc_final: 0.4903 (mtm) REVERT: 4 261 PHE cc_start: 0.5515 (t80) cc_final: 0.5171 (m-80) REVERT: 4 365 PHE cc_start: 0.4484 (t80) cc_final: 0.4122 (t80) REVERT: 5 41 TYR cc_start: 0.6839 (t80) cc_final: 0.6567 (t80) REVERT: 5 190 ASP cc_start: 0.7848 (t0) cc_final: 0.7647 (t0) REVERT: 6 44 LEU cc_start: 0.8868 (tp) cc_final: 0.8564 (tp) REVERT: 6 141 TYR cc_start: 0.8807 (m-80) cc_final: 0.8244 (m-80) REVERT: 7 187 ILE cc_start: 0.8428 (mm) cc_final: 0.8097 (mt) REVERT: 7 192 TRP cc_start: 0.7648 (t-100) cc_final: 0.7416 (t-100) REVERT: 9 37 ARG cc_start: 0.8086 (ptm160) cc_final: 0.7776 (ptp-110) REVERT: 9 53 GLU cc_start: 0.8575 (pt0) cc_final: 0.7935 (tm-30) REVERT: 9 56 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8218 (ptpp) REVERT: 9 75 ILE cc_start: 0.9164 (mm) cc_final: 0.8911 (mm) REVERT: D 374 CYS cc_start: 0.6679 (m) cc_final: 0.6445 (m) REVERT: E 325 MET cc_start: 0.8511 (ppp) cc_final: 0.7675 (ptt) REVERT: G 325 MET cc_start: 0.7909 (mmm) cc_final: 0.7567 (mmm) REVERT: J 153 MET cc_start: 0.7896 (tmm) cc_final: 0.7585 (tmm) REVERT: N 81 ASP cc_start: 0.7489 (m-30) cc_final: 0.7081 (m-30) REVERT: N 101 PRO cc_start: 0.8080 (Cg_exo) cc_final: 0.7855 (Cg_endo) REVERT: Q 61 THR cc_start: 0.8763 (m) cc_final: 0.8463 (m) REVERT: Q 117 ASP cc_start: 0.8241 (t0) cc_final: 0.7528 (t0) REVERT: Q 121 GLN cc_start: 0.8328 (tp40) cc_final: 0.8098 (tm-30) REVERT: R 81 ASP cc_start: 0.8064 (m-30) cc_final: 0.7832 (m-30) REVERT: R 117 ASP cc_start: 0.7968 (t70) cc_final: 0.7738 (t0) REVERT: T 81 ASP cc_start: 0.7692 (m-30) cc_final: 0.7302 (m-30) REVERT: U 240 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6445 (pt0) REVERT: V 91 MET cc_start: 0.7796 (mmm) cc_final: 0.7485 (tmm) REVERT: V 152 SER cc_start: 0.8323 (t) cc_final: 0.8039 (p) REVERT: Z 34 PHE cc_start: 0.8138 (p90) cc_final: 0.7929 (p90) REVERT: Z 46 ARG cc_start: 0.6140 (ttp-170) cc_final: 0.5654 (ttp80) REVERT: Z 50 TYR cc_start: 0.7346 (m-80) cc_final: 0.6980 (m-80) REVERT: Z 84 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8229 (mm-30) outliers start: 45 outliers final: 33 residues processed: 670 average time/residue: 0.5543 time to fit residues: 647.7830 Evaluate side-chains 625 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 592 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 326 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 376 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 563 optimal weight: 4.9990 chunk 461 optimal weight: 4.9990 chunk 186 optimal weight: 0.0870 chunk 678 optimal weight: 2.9990 chunk 733 optimal weight: 6.9990 chunk 604 optimal weight: 5.9990 chunk 673 optimal weight: 9.9990 chunk 231 optimal weight: 4.9990 chunk 544 optimal weight: 0.0170 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS 2 163 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN B 121 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN T 129 HIS V 32 GLN V 231 HIS Y 296 ASN Z 21 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 61482 Z= 0.186 Angle : 0.541 9.851 83150 Z= 0.268 Chirality : 0.041 0.179 9290 Planarity : 0.004 0.048 10688 Dihedral : 5.524 75.961 8390 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.05 % Allowed : 7.63 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.10), residues: 7524 helix: 1.62 (0.09), residues: 3670 sheet: 0.40 (0.17), residues: 872 loop : 0.21 (0.12), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 161 HIS 0.006 0.001 HIS 1 241 PHE 0.025 0.001 PHE B 279 TYR 0.025 0.001 TYR 7 147 ARG 0.005 0.000 ARG Q 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 636 time to evaluate : 5.266 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: 1 302 HIS cc_start: 0.5615 (t-90) cc_final: 0.5271 (t-170) REVERT: 1 383 MET cc_start: 0.8346 (mmp) cc_final: 0.8062 (mmp) REVERT: 2 251 MET cc_start: 0.1659 (tpt) cc_final: 0.0072 (ptm) REVERT: 3 111 MET cc_start: 0.5649 (mmt) cc_final: 0.4940 (mtm) REVERT: 3 239 MET cc_start: 0.1566 (tpt) cc_final: 0.1157 (mmm) REVERT: 4 202 PHE cc_start: 0.5550 (m-80) cc_final: 0.4962 (t80) REVERT: 4 261 PHE cc_start: 0.5461 (t80) cc_final: 0.5196 (m-80) REVERT: 5 41 TYR cc_start: 0.7002 (t80) cc_final: 0.6727 (t80) REVERT: 5 190 ASP cc_start: 0.7935 (t0) cc_final: 0.7628 (t0) REVERT: 5 202 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8218 (mm-30) REVERT: 6 141 TYR cc_start: 0.8891 (m-80) cc_final: 0.8347 (m-80) REVERT: 7 139 ASN cc_start: 0.6817 (m-40) cc_final: 0.5619 (m-40) REVERT: 7 187 ILE cc_start: 0.8485 (mm) cc_final: 0.8167 (mt) REVERT: 9 37 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7545 (ptp-110) REVERT: 9 53 GLU cc_start: 0.8449 (pt0) cc_final: 0.7791 (tm-30) REVERT: 9 75 ILE cc_start: 0.9210 (mm) cc_final: 0.8995 (mm) REVERT: A 49 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: B 283 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7701 (mpp) REVERT: E 78 ASN cc_start: 0.8108 (t0) cc_final: 0.7877 (t0) REVERT: E 325 MET cc_start: 0.8525 (ppp) cc_final: 0.7755 (ptp) REVERT: F 132 MET cc_start: 0.8307 (ppp) cc_final: 0.7898 (ppp) REVERT: N 81 ASP cc_start: 0.7486 (m-30) cc_final: 0.7128 (m-30) REVERT: N 101 PRO cc_start: 0.8074 (Cg_exo) cc_final: 0.7835 (Cg_endo) REVERT: Q 61 THR cc_start: 0.8687 (m) cc_final: 0.8384 (m) REVERT: Q 117 ASP cc_start: 0.8296 (t0) cc_final: 0.7546 (t0) REVERT: Q 121 GLN cc_start: 0.8484 (tp40) cc_final: 0.8031 (tm-30) REVERT: R 84 ASP cc_start: 0.7946 (t0) cc_final: 0.7727 (t0) REVERT: R 117 ASP cc_start: 0.7942 (t70) cc_final: 0.7671 (t0) REVERT: S 41 GLU cc_start: 0.8196 (pt0) cc_final: 0.7832 (tm-30) REVERT: S 125 GLU cc_start: 0.7933 (mm-30) cc_final: 0.6951 (mt-10) REVERT: T 81 ASP cc_start: 0.7665 (m-30) cc_final: 0.7232 (m-30) REVERT: U 126 TYR cc_start: 0.7685 (t80) cc_final: 0.7445 (t80) REVERT: U 164 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: V 152 SER cc_start: 0.8348 (t) cc_final: 0.8049 (p) REVERT: Z 84 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8234 (mm-30) outliers start: 69 outliers final: 48 residues processed: 673 average time/residue: 0.5404 time to fit residues: 636.8649 Evaluate side-chains 639 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 588 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 200 ILE Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 670 optimal weight: 0.9980 chunk 510 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 323 optimal weight: 4.9990 chunk 455 optimal weight: 0.8980 chunk 681 optimal weight: 0.9980 chunk 721 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 645 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 308 HIS C 111 ASN D 12 ASN D 40 HIS E 12 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS V 231 HIS Y 334 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 61482 Z= 0.183 Angle : 0.531 9.768 83150 Z= 0.261 Chirality : 0.040 0.166 9290 Planarity : 0.004 0.046 10688 Dihedral : 5.386 76.223 8390 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.41 % Allowed : 8.79 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 7524 helix: 1.81 (0.09), residues: 3679 sheet: 0.44 (0.18), residues: 872 loop : 0.23 (0.12), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 4 241 HIS 0.009 0.001 HIS 1 241 PHE 0.023 0.001 PHE Z 94 TYR 0.023 0.001 TYR 6 41 ARG 0.005 0.000 ARG P 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 614 time to evaluate : 5.247 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: 1 302 HIS cc_start: 0.5627 (t-90) cc_final: 0.5009 (t-170) REVERT: 1 383 MET cc_start: 0.8390 (mmp) cc_final: 0.8094 (mmp) REVERT: 2 251 MET cc_start: 0.1299 (tpt) cc_final: -0.0009 (ptm) REVERT: 3 111 MET cc_start: 0.5704 (mmt) cc_final: 0.4880 (mtm) REVERT: 3 239 MET cc_start: 0.1723 (tpt) cc_final: 0.1265 (mmm) REVERT: 4 151 GLN cc_start: 0.6465 (pt0) cc_final: 0.5893 (pm20) REVERT: 4 202 PHE cc_start: 0.5549 (m-80) cc_final: 0.4965 (t80) REVERT: 4 265 MET cc_start: 0.1317 (mmp) cc_final: -0.0704 (mmm) REVERT: 5 41 TYR cc_start: 0.7012 (t80) cc_final: 0.6747 (t80) REVERT: 5 162 LEU cc_start: 0.8081 (mm) cc_final: 0.7833 (pt) REVERT: 5 202 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8127 (mm-30) REVERT: 6 141 TYR cc_start: 0.8883 (m-80) cc_final: 0.8314 (m-80) REVERT: 7 139 ASN cc_start: 0.6784 (m-40) cc_final: 0.6394 (m-40) REVERT: 9 37 ARG cc_start: 0.8020 (ptm160) cc_final: 0.7471 (ptp-110) REVERT: 9 53 GLU cc_start: 0.8387 (pt0) cc_final: 0.7715 (tm-30) REVERT: 9 75 ILE cc_start: 0.9184 (mm) cc_final: 0.8981 (mm) REVERT: B 283 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7751 (mpp) REVERT: E 78 ASN cc_start: 0.8055 (t0) cc_final: 0.7788 (t0) REVERT: E 325 MET cc_start: 0.8490 (ppp) cc_final: 0.7835 (ptp) REVERT: H 47 MET cc_start: 0.5543 (ppp) cc_final: 0.5270 (ppp) REVERT: J 305 MET cc_start: 0.9361 (mmm) cc_final: 0.9113 (tpp) REVERT: M 114 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7642 (tm-30) REVERT: N 81 ASP cc_start: 0.7470 (m-30) cc_final: 0.7129 (m-30) REVERT: N 101 PRO cc_start: 0.8057 (Cg_exo) cc_final: 0.7812 (Cg_endo) REVERT: Q 61 THR cc_start: 0.8738 (m) cc_final: 0.8424 (m) REVERT: Q 117 ASP cc_start: 0.8309 (t0) cc_final: 0.7522 (t0) REVERT: Q 121 GLN cc_start: 0.8530 (tp40) cc_final: 0.8044 (tm-30) REVERT: R 117 ASP cc_start: 0.7879 (t70) cc_final: 0.7588 (t0) REVERT: S 41 GLU cc_start: 0.8199 (pt0) cc_final: 0.7833 (tm-30) REVERT: S 158 GLN cc_start: 0.7328 (tp40) cc_final: 0.6987 (tp40) REVERT: T 41 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8323 (mm-30) REVERT: T 81 ASP cc_start: 0.7648 (m-30) cc_final: 0.7154 (m-30) REVERT: U 164 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7086 (tmm) REVERT: V 152 SER cc_start: 0.8364 (t) cc_final: 0.8061 (p) REVERT: Z 26 PHE cc_start: 0.8136 (t80) cc_final: 0.7867 (t80) REVERT: Z 84 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8214 (mm-30) outliers start: 92 outliers final: 66 residues processed: 670 average time/residue: 0.5312 time to fit residues: 620.0009 Evaluate side-chains 651 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 583 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 200 ILE Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 5 residue 161 HIS Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 16 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 61 THR Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 231 HIS Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 600 optimal weight: 0.9980 chunk 409 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 536 optimal weight: 0.5980 chunk 297 optimal weight: 0.4980 chunk 615 optimal weight: 3.9990 chunk 498 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 368 optimal weight: 0.2980 chunk 647 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN E 12 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 HIS ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 61482 Z= 0.152 Angle : 0.518 9.918 83150 Z= 0.255 Chirality : 0.040 0.152 9290 Planarity : 0.003 0.045 10688 Dihedral : 5.283 76.533 8390 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.22 % Allowed : 9.91 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.10), residues: 7524 helix: 1.92 (0.09), residues: 3691 sheet: 0.45 (0.18), residues: 873 loop : 0.28 (0.12), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 7 192 HIS 0.016 0.001 HIS V 231 PHE 0.020 0.001 PHE Z 94 TYR 0.026 0.001 TYR 6 41 ARG 0.006 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 614 time to evaluate : 5.224 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: symmetry clash REVERT: 1 302 HIS cc_start: 0.5629 (t-90) cc_final: 0.5022 (t-170) REVERT: 1 383 MET cc_start: 0.8456 (mmp) cc_final: 0.8156 (mmp) REVERT: 2 251 MET cc_start: 0.1227 (tpt) cc_final: 0.0032 (ptm) REVERT: 3 111 MET cc_start: 0.6180 (mmt) cc_final: 0.5220 (mtm) REVERT: 3 239 MET cc_start: 0.1727 (tpt) cc_final: 0.1274 (mmm) REVERT: 4 151 GLN cc_start: 0.6477 (pt0) cc_final: 0.5891 (pm20) REVERT: 4 165 GLN cc_start: 0.1924 (OUTLIER) cc_final: 0.0988 (pm20) REVERT: 4 202 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.4981 (t80) REVERT: 5 162 LEU cc_start: 0.7989 (mm) cc_final: 0.7754 (pt) REVERT: 5 202 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8109 (mm-30) REVERT: 7 139 ASN cc_start: 0.6637 (m-40) cc_final: 0.6394 (m110) REVERT: 7 169 GLU cc_start: 0.8501 (pp20) cc_final: 0.8110 (pp20) REVERT: 9 53 GLU cc_start: 0.8410 (pt0) cc_final: 0.7771 (tm-30) REVERT: 9 56 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8314 (ptpp) REVERT: 9 75 ILE cc_start: 0.9162 (mm) cc_final: 0.8953 (mm) REVERT: E 78 ASN cc_start: 0.7991 (t0) cc_final: 0.7723 (t0) REVERT: E 313 MET cc_start: 0.8458 (ttm) cc_final: 0.8062 (mtp) REVERT: E 325 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7824 (ptp) REVERT: F 132 MET cc_start: 0.8141 (ppp) cc_final: 0.7878 (ppp) REVERT: J 305 MET cc_start: 0.9350 (mmm) cc_final: 0.9110 (tpp) REVERT: N 81 ASP cc_start: 0.7441 (m-30) cc_final: 0.7092 (m-30) REVERT: N 101 PRO cc_start: 0.8117 (Cg_exo) cc_final: 0.7854 (Cg_endo) REVERT: Q 61 THR cc_start: 0.8711 (m) cc_final: 0.8392 (m) REVERT: Q 121 GLN cc_start: 0.8490 (tp40) cc_final: 0.8237 (tp40) REVERT: R 87 MET cc_start: 0.7647 (mmp) cc_final: 0.7443 (mmp) REVERT: R 117 ASP cc_start: 0.7800 (t70) cc_final: 0.7561 (t0) REVERT: S 41 GLU cc_start: 0.8218 (pt0) cc_final: 0.7680 (tm-30) REVERT: S 98 GLU cc_start: 0.7628 (mp0) cc_final: 0.7293 (pm20) REVERT: T 81 ASP cc_start: 0.7626 (m-30) cc_final: 0.7139 (m-30) REVERT: T 98 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: U 164 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7110 (tmm) REVERT: V 152 SER cc_start: 0.8374 (t) cc_final: 0.8074 (p) REVERT: Z 84 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8196 (mm-30) outliers start: 80 outliers final: 63 residues processed: 652 average time/residue: 0.5234 time to fit residues: 597.6168 Evaluate side-chains 661 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 593 time to evaluate : 5.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 200 ILE Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 165 GLN Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain N residue 124 LYS Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 98 GLU Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 242 optimal weight: 0.8980 chunk 649 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 423 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 721 optimal weight: 0.5980 chunk 599 optimal weight: 0.9980 chunk 334 optimal weight: 0.0050 chunk 60 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN E 12 ASN E 41 GLN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 61482 Z= 0.154 Angle : 0.518 10.897 83150 Z= 0.253 Chirality : 0.040 0.154 9290 Planarity : 0.003 0.060 10688 Dihedral : 5.162 79.189 8390 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.36 % Allowed : 10.42 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.10), residues: 7524 helix: 2.04 (0.09), residues: 3685 sheet: 0.46 (0.18), residues: 880 loop : 0.32 (0.12), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.004 0.001 HIS D 40 PHE 0.028 0.001 PHE B 279 TYR 0.033 0.001 TYR V 178 ARG 0.005 0.000 ARG 5 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 618 time to evaluate : 5.268 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: 1 302 HIS cc_start: 0.5618 (t-90) cc_final: 0.5008 (t-170) REVERT: 1 383 MET cc_start: 0.8441 (mmp) cc_final: 0.8163 (mmp) REVERT: 2 251 MET cc_start: 0.1208 (tpt) cc_final: -0.0098 (ptp) REVERT: 3 111 MET cc_start: 0.6195 (mmt) cc_final: 0.4817 (mtm) REVERT: 3 112 MET cc_start: 0.6565 (pmm) cc_final: 0.3809 (ttt) REVERT: 3 239 MET cc_start: 0.1652 (tpt) cc_final: 0.1206 (mmm) REVERT: 4 165 GLN cc_start: 0.2003 (OUTLIER) cc_final: 0.1082 (pm20) REVERT: 4 202 PHE cc_start: 0.5538 (OUTLIER) cc_final: 0.4984 (t80) REVERT: 4 261 PHE cc_start: 0.6364 (t80) cc_final: 0.5983 (m-80) REVERT: 5 202 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8042 (mm-30) REVERT: 9 53 GLU cc_start: 0.8452 (pt0) cc_final: 0.7815 (tm-30) REVERT: 9 56 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8250 (ptpp) REVERT: 9 75 ILE cc_start: 0.9156 (mm) cc_final: 0.8952 (mm) REVERT: B 283 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6337 (mpp) REVERT: D 313 MET cc_start: 0.8444 (ttm) cc_final: 0.8244 (mtp) REVERT: E 78 ASN cc_start: 0.7982 (t0) cc_final: 0.7675 (t0) REVERT: E 313 MET cc_start: 0.8545 (ttm) cc_final: 0.8158 (mtp) REVERT: E 325 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7899 (ptp) REVERT: F 132 MET cc_start: 0.8160 (ppp) cc_final: 0.7905 (ppp) REVERT: G 16 MET cc_start: 0.8063 (mtp) cc_final: 0.7721 (mtt) REVERT: I 283 MET cc_start: 0.8104 (mmt) cc_final: 0.7784 (mpp) REVERT: J 305 MET cc_start: 0.9347 (mmm) cc_final: 0.9106 (tpp) REVERT: K 283 MET cc_start: 0.8479 (mmm) cc_final: 0.8195 (mmm) REVERT: N 81 ASP cc_start: 0.7427 (m-30) cc_final: 0.7113 (m-30) REVERT: N 84 ASP cc_start: 0.8104 (t0) cc_final: 0.7699 (t0) REVERT: N 101 PRO cc_start: 0.8097 (Cg_exo) cc_final: 0.7839 (Cg_endo) REVERT: P 53 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6838 (pm20) REVERT: Q 61 THR cc_start: 0.8728 (m) cc_final: 0.8409 (m) REVERT: Q 121 GLN cc_start: 0.8428 (tp40) cc_final: 0.8149 (tp40) REVERT: R 117 ASP cc_start: 0.7848 (t70) cc_final: 0.7599 (t0) REVERT: S 41 GLU cc_start: 0.8130 (pt0) cc_final: 0.7846 (tm-30) REVERT: S 81 ASP cc_start: 0.8896 (m-30) cc_final: 0.8647 (m-30) REVERT: S 98 GLU cc_start: 0.7557 (mp0) cc_final: 0.7292 (pm20) REVERT: T 81 ASP cc_start: 0.7632 (m-30) cc_final: 0.7145 (m-30) REVERT: T 98 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: U 164 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7108 (tmm) REVERT: U 237 MET cc_start: 0.5460 (tmm) cc_final: 0.5240 (tmm) REVERT: U 240 GLN cc_start: 0.6790 (mm-40) cc_final: 0.6571 (pt0) REVERT: V 152 SER cc_start: 0.8384 (t) cc_final: 0.8080 (p) REVERT: V 231 HIS cc_start: 0.6798 (t-90) cc_final: 0.6459 (m-70) REVERT: Z 36 GLU cc_start: 0.7504 (pm20) cc_final: 0.7012 (pm20) REVERT: Z 84 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8193 (mm-30) outliers start: 89 outliers final: 65 residues processed: 664 average time/residue: 0.5278 time to fit residues: 612.2318 Evaluate side-chains 662 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 590 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 200 ILE Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 165 ILE Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 165 GLN Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 67 HIS Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 98 GLU Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 695 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 411 optimal weight: 2.9990 chunk 527 optimal weight: 0.9980 chunk 408 optimal weight: 0.6980 chunk 607 optimal weight: 2.9990 chunk 403 optimal weight: 1.9990 chunk 719 optimal weight: 0.0370 chunk 449 optimal weight: 4.9990 chunk 438 optimal weight: 0.3980 chunk 331 optimal weight: 6.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 12 ASN E 41 GLN ** K 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 61482 Z= 0.151 Angle : 0.514 11.391 83150 Z= 0.251 Chirality : 0.040 0.159 9290 Planarity : 0.003 0.045 10688 Dihedral : 5.067 76.787 8390 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.35 % Allowed : 11.01 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7524 helix: 2.10 (0.09), residues: 3689 sheet: 0.48 (0.18), residues: 880 loop : 0.35 (0.12), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 7 192 HIS 0.004 0.000 HIS D 40 PHE 0.027 0.001 PHE Z 94 TYR 0.031 0.001 TYR 6 41 ARG 0.003 0.000 ARG 5 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 616 time to evaluate : 5.238 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: 1 302 HIS cc_start: 0.5309 (t-90) cc_final: 0.4773 (t-170) REVERT: 1 383 MET cc_start: 0.8437 (mmp) cc_final: 0.8170 (mmp) REVERT: 2 251 MET cc_start: 0.1145 (tpt) cc_final: -0.0093 (ptp) REVERT: 3 111 MET cc_start: 0.6188 (mmt) cc_final: 0.4848 (mtm) REVERT: 3 112 MET cc_start: 0.6572 (pmm) cc_final: 0.3809 (ttt) REVERT: 3 239 MET cc_start: 0.1655 (tpt) cc_final: 0.1346 (mmm) REVERT: 4 165 GLN cc_start: 0.2078 (OUTLIER) cc_final: 0.1160 (pm20) REVERT: 4 202 PHE cc_start: 0.5531 (OUTLIER) cc_final: 0.4979 (t80) REVERT: 4 261 PHE cc_start: 0.6355 (t80) cc_final: 0.5977 (m-80) REVERT: 5 202 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8060 (mm-30) REVERT: 9 53 GLU cc_start: 0.8330 (pt0) cc_final: 0.7769 (tm-30) REVERT: 9 56 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8281 (ptpp) REVERT: A 44 MET cc_start: 0.3345 (tmm) cc_final: 0.3111 (tmm) REVERT: B 64 ILE cc_start: 0.9069 (pt) cc_final: 0.8676 (tp) REVERT: B 283 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6554 (mpt) REVERT: C 82 MET cc_start: 0.8702 (mmm) cc_final: 0.8422 (tpt) REVERT: E 78 ASN cc_start: 0.7981 (t0) cc_final: 0.7687 (t0) REVERT: E 313 MET cc_start: 0.8638 (ttm) cc_final: 0.8298 (ttt) REVERT: E 325 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7951 (ptp) REVERT: F 132 MET cc_start: 0.8148 (ppp) cc_final: 0.7892 (ppp) REVERT: G 16 MET cc_start: 0.8041 (mtp) cc_final: 0.7699 (mtt) REVERT: I 283 MET cc_start: 0.8114 (mmt) cc_final: 0.7736 (mpp) REVERT: J 305 MET cc_start: 0.9344 (mmm) cc_final: 0.9105 (tpp) REVERT: N 81 ASP cc_start: 0.7424 (m-30) cc_final: 0.7103 (m-30) REVERT: N 84 ASP cc_start: 0.8132 (t0) cc_final: 0.7844 (t0) REVERT: N 101 PRO cc_start: 0.8093 (Cg_exo) cc_final: 0.7834 (Cg_endo) REVERT: O 77 ASP cc_start: 0.7702 (t70) cc_final: 0.7417 (p0) REVERT: P 53 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: Q 61 THR cc_start: 0.8654 (m) cc_final: 0.8368 (m) REVERT: Q 121 GLN cc_start: 0.8428 (tp40) cc_final: 0.8137 (tp40) REVERT: R 117 ASP cc_start: 0.7831 (t70) cc_final: 0.7557 (t0) REVERT: S 41 GLU cc_start: 0.8105 (pt0) cc_final: 0.7840 (tm-30) REVERT: S 81 ASP cc_start: 0.8825 (m-30) cc_final: 0.8569 (m-30) REVERT: S 98 GLU cc_start: 0.7542 (mp0) cc_final: 0.7312 (pm20) REVERT: T 81 ASP cc_start: 0.7627 (m-30) cc_final: 0.7154 (m-30) REVERT: U 126 TYR cc_start: 0.7858 (t80) cc_final: 0.7561 (t80) REVERT: U 164 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7085 (tmm) REVERT: U 248 MET cc_start: -0.1718 (OUTLIER) cc_final: -0.2060 (ptt) REVERT: V 152 SER cc_start: 0.8391 (t) cc_final: 0.8086 (p) REVERT: Z 35 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6730 (tm-30) REVERT: Z 84 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8183 (mm-30) outliers start: 88 outliers final: 66 residues processed: 659 average time/residue: 0.5335 time to fit residues: 619.4868 Evaluate side-chains 666 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 593 time to evaluate : 5.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 165 ILE Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 4 residue 165 GLN Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain K residue 54 VAL Chi-restraints excluded: chain K residue 68 LYS Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain R residue 67 HIS Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 135 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 444 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 429 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 457 optimal weight: 3.9990 chunk 489 optimal weight: 0.0980 chunk 355 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 565 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 163 HIS 1 375 GLN ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN G 12 ASN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 61482 Z= 0.209 Angle : 0.549 11.766 83150 Z= 0.269 Chirality : 0.041 0.164 9290 Planarity : 0.004 0.046 10688 Dihedral : 5.050 77.837 8390 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.47 % Allowed : 11.31 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.10), residues: 7524 helix: 2.09 (0.09), residues: 3678 sheet: 0.47 (0.18), residues: 874 loop : 0.34 (0.12), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 7 192 HIS 0.012 0.001 HIS 3 308 PHE 0.029 0.001 PHE Z 94 TYR 0.036 0.001 TYR 6 41 ARG 0.006 0.000 ARG 5 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 615 time to evaluate : 5.257 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: symmetry clash REVERT: 1 302 HIS cc_start: 0.5313 (t-90) cc_final: 0.4778 (t-170) REVERT: 2 251 MET cc_start: 0.1281 (tpt) cc_final: -0.0256 (ptp) REVERT: 2 288 LYS cc_start: 0.6768 (mmtt) cc_final: 0.6154 (pptt) REVERT: 3 111 MET cc_start: 0.6244 (mmt) cc_final: 0.5351 (ptp) REVERT: 3 216 TYR cc_start: 0.5149 (m-80) cc_final: 0.4810 (t80) REVERT: 3 241 TRP cc_start: 0.4187 (OUTLIER) cc_final: 0.3773 (m-90) REVERT: 4 165 GLN cc_start: 0.2283 (OUTLIER) cc_final: 0.1391 (pm20) REVERT: 4 202 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5117 (t80) REVERT: 4 261 PHE cc_start: 0.6336 (t80) cc_final: 0.5937 (m-80) REVERT: 5 198 LEU cc_start: 0.8001 (mt) cc_final: 0.7665 (mt) REVERT: 5 202 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8052 (mm-30) REVERT: 7 62 MET cc_start: 0.8312 (mtp) cc_final: 0.7836 (mtt) REVERT: 7 132 GLU cc_start: 0.6991 (tp30) cc_final: 0.6406 (tp30) REVERT: 9 53 GLU cc_start: 0.8383 (pt0) cc_final: 0.7774 (tm-30) REVERT: A 44 MET cc_start: 0.3638 (tmm) cc_final: 0.3421 (tmm) REVERT: B 64 ILE cc_start: 0.9078 (pt) cc_final: 0.8677 (tp) REVERT: B 82 MET cc_start: 0.8731 (mmm) cc_final: 0.8181 (tpt) REVERT: B 283 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6830 (mpt) REVERT: C 82 MET cc_start: 0.8793 (mmm) cc_final: 0.8503 (tpt) REVERT: E 78 ASN cc_start: 0.8043 (t0) cc_final: 0.7653 (t0) REVERT: E 313 MET cc_start: 0.8638 (ttm) cc_final: 0.8426 (ttm) REVERT: E 325 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8071 (ptp) REVERT: G 16 MET cc_start: 0.8046 (mtp) cc_final: 0.7771 (mtt) REVERT: J 305 MET cc_start: 0.9366 (mmm) cc_final: 0.9121 (tpp) REVERT: J 325 MET cc_start: 0.8389 (mmm) cc_final: 0.8125 (mmm) REVERT: N 67 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7222 (t-90) REVERT: N 81 ASP cc_start: 0.7461 (m-30) cc_final: 0.7111 (m-30) REVERT: N 84 ASP cc_start: 0.8147 (t0) cc_final: 0.7814 (t0) REVERT: N 101 PRO cc_start: 0.8132 (Cg_exo) cc_final: 0.7881 (Cg_endo) REVERT: N 125 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8207 (tm-30) REVERT: O 114 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: Q 61 THR cc_start: 0.8747 (m) cc_final: 0.8459 (m) REVERT: Q 117 ASP cc_start: 0.8264 (t0) cc_final: 0.7517 (t0) REVERT: Q 121 GLN cc_start: 0.8445 (tp40) cc_final: 0.8146 (tp40) REVERT: R 87 MET cc_start: 0.7428 (mmp) cc_final: 0.7209 (tpp) REVERT: R 117 ASP cc_start: 0.7891 (t70) cc_final: 0.7635 (t0) REVERT: S 41 GLU cc_start: 0.8129 (pt0) cc_final: 0.7864 (tm-30) REVERT: S 98 GLU cc_start: 0.7506 (mp0) cc_final: 0.7263 (pm20) REVERT: T 51 GLU cc_start: 0.7571 (mp0) cc_final: 0.7269 (mp0) REVERT: T 81 ASP cc_start: 0.7656 (m-30) cc_final: 0.7197 (m-30) REVERT: U 164 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7115 (tmm) REVERT: U 248 MET cc_start: -0.1182 (OUTLIER) cc_final: -0.1447 (ptt) REVERT: V 152 SER cc_start: 0.8410 (t) cc_final: 0.8094 (p) REVERT: Z 35 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7154 (mt-10) REVERT: Z 84 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8244 (mm-30) outliers start: 96 outliers final: 65 residues processed: 666 average time/residue: 0.5303 time to fit residues: 618.4431 Evaluate side-chains 668 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 594 time to evaluate : 5.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 165 ILE Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 3 residue 304 TYR Chi-restraints excluded: chain 3 residue 523 VAL Chi-restraints excluded: chain 4 residue 165 GLN Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 9 residue 40 ASN Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 654 optimal weight: 7.9990 chunk 688 optimal weight: 5.9990 chunk 628 optimal weight: 0.9990 chunk 670 optimal weight: 3.9990 chunk 403 optimal weight: 1.9990 chunk 291 optimal weight: 0.7980 chunk 526 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 605 optimal weight: 1.9990 chunk 633 optimal weight: 2.9990 chunk 667 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 375 GLN ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 375 GLN ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN J 137 GLN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 HIS ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 HIS Y 53 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 61482 Z= 0.228 Angle : 0.564 12.470 83150 Z= 0.277 Chirality : 0.041 0.175 9290 Planarity : 0.004 0.047 10688 Dihedral : 5.036 74.136 8390 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.38 % Allowed : 11.51 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.10), residues: 7524 helix: 2.07 (0.09), residues: 3677 sheet: 0.39 (0.18), residues: 889 loop : 0.34 (0.12), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 7 192 HIS 0.015 0.001 HIS 3 308 PHE 0.030 0.001 PHE Z 94 TYR 0.039 0.001 TYR 6 41 ARG 0.008 0.000 ARG 1 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 606 time to evaluate : 5.372 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: 1 123 MET cc_start: 0.7138 (tmm) cc_final: 0.5712 (tpt) REVERT: 1 302 HIS cc_start: 0.5362 (t-90) cc_final: 0.4803 (t-170) REVERT: 2 251 MET cc_start: 0.1380 (tpt) cc_final: -0.0207 (ptp) REVERT: 2 288 LYS cc_start: 0.6799 (mmtt) cc_final: 0.6295 (pptt) REVERT: 3 111 MET cc_start: 0.6330 (mmt) cc_final: 0.4819 (ptm) REVERT: 3 112 MET cc_start: 0.6685 (pmm) cc_final: 0.3857 (ttt) REVERT: 4 165 GLN cc_start: 0.2337 (OUTLIER) cc_final: 0.1436 (pm20) REVERT: 4 202 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5109 (t80) REVERT: 5 198 LEU cc_start: 0.8023 (mt) cc_final: 0.7714 (mt) REVERT: 5 202 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8070 (mm-30) REVERT: 7 62 MET cc_start: 0.8504 (mtp) cc_final: 0.8033 (mtt) REVERT: 7 132 GLU cc_start: 0.6998 (tp30) cc_final: 0.6377 (tp30) REVERT: 9 53 GLU cc_start: 0.8516 (pt0) cc_final: 0.7857 (tm-30) REVERT: B 64 ILE cc_start: 0.9088 (pt) cc_final: 0.8673 (tp) REVERT: B 283 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.6898 (mpt) REVERT: C 82 MET cc_start: 0.8789 (mmm) cc_final: 0.8500 (tpt) REVERT: D 374 CYS cc_start: 0.7209 (m) cc_final: 0.6966 (m) REVERT: E 78 ASN cc_start: 0.8006 (t0) cc_final: 0.7615 (t0) REVERT: G 16 MET cc_start: 0.8070 (mtp) cc_final: 0.7792 (mtt) REVERT: H 132 MET cc_start: 0.7569 (ttp) cc_final: 0.7270 (ttp) REVERT: J 305 MET cc_start: 0.9340 (mmm) cc_final: 0.9106 (tpp) REVERT: N 67 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7387 (t-90) REVERT: N 81 ASP cc_start: 0.7458 (m-30) cc_final: 0.7138 (m-30) REVERT: N 84 ASP cc_start: 0.8208 (t0) cc_final: 0.7865 (t0) REVERT: N 125 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8172 (tm-30) REVERT: O 114 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: Q 61 THR cc_start: 0.8851 (m) cc_final: 0.8590 (m) REVERT: Q 117 ASP cc_start: 0.8265 (t0) cc_final: 0.7815 (t70) REVERT: Q 121 GLN cc_start: 0.8433 (tp40) cc_final: 0.8154 (tp40) REVERT: R 87 MET cc_start: 0.7446 (mmp) cc_final: 0.7221 (tpp) REVERT: R 117 ASP cc_start: 0.7950 (t70) cc_final: 0.7639 (t0) REVERT: R 121 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8984 (tm-30) REVERT: S 41 GLU cc_start: 0.8153 (pt0) cc_final: 0.7878 (tm-30) REVERT: T 51 GLU cc_start: 0.7529 (mp0) cc_final: 0.7202 (mp0) REVERT: T 81 ASP cc_start: 0.7662 (m-30) cc_final: 0.7167 (m-30) REVERT: T 98 GLU cc_start: 0.8195 (mp0) cc_final: 0.7851 (mp0) REVERT: U 164 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7097 (tmm) REVERT: U 248 MET cc_start: -0.0368 (OUTLIER) cc_final: -0.0607 (ptt) REVERT: V 152 SER cc_start: 0.8467 (t) cc_final: 0.8141 (p) REVERT: Y 247 MET cc_start: 0.8781 (ttm) cc_final: 0.8555 (ttm) REVERT: Z 28 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8417 (mt-10) REVERT: Z 35 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7295 (mt-10) REVERT: Z 84 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8210 (mm-30) REVERT: Z 87 GLU cc_start: 0.7236 (tt0) cc_final: 0.7009 (tt0) outliers start: 90 outliers final: 69 residues processed: 654 average time/residue: 0.5364 time to fit residues: 612.8195 Evaluate side-chains 663 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 587 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 165 ILE Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 3 residue 523 VAL Chi-restraints excluded: chain 4 residue 165 GLN Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 305 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 164 MET Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 439 optimal weight: 0.8980 chunk 708 optimal weight: 5.9990 chunk 432 optimal weight: 0.9990 chunk 336 optimal weight: 0.3980 chunk 492 optimal weight: 3.9990 chunk 743 optimal weight: 5.9990 chunk 684 optimal weight: 6.9990 chunk 591 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 457 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 241 HIS ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN E 12 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN M 34 ASN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 61482 Z= 0.189 Angle : 0.556 13.075 83150 Z= 0.272 Chirality : 0.041 0.217 9290 Planarity : 0.003 0.047 10688 Dihedral : 4.973 74.114 8390 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 11.83 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.10), residues: 7524 helix: 2.10 (0.09), residues: 3690 sheet: 0.40 (0.18), residues: 888 loop : 0.37 (0.12), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 7 192 HIS 0.012 0.001 HIS 3 308 PHE 0.030 0.001 PHE Z 94 TYR 0.037 0.001 TYR 6 41 ARG 0.006 0.000 ARG 5 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15048 Ramachandran restraints generated. 7524 Oldfield, 0 Emsley, 7524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 596 time to evaluate : 5.642 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: 1 123 MET cc_start: 0.7182 (tmm) cc_final: 0.5766 (tpt) REVERT: 1 302 HIS cc_start: 0.5328 (t-90) cc_final: 0.4803 (t-170) REVERT: 2 251 MET cc_start: 0.1447 (tpt) cc_final: -0.0260 (ptp) REVERT: 2 288 LYS cc_start: 0.6838 (mmtt) cc_final: 0.6329 (pptt) REVERT: 3 111 MET cc_start: 0.6271 (mmt) cc_final: 0.5222 (ptm) REVERT: 3 216 TYR cc_start: 0.5231 (m-80) cc_final: 0.4884 (t80) REVERT: 4 151 GLN cc_start: 0.6259 (pt0) cc_final: 0.5609 (pm20) REVERT: 4 202 PHE cc_start: 0.5410 (OUTLIER) cc_final: 0.4973 (t80) REVERT: 5 198 LEU cc_start: 0.8012 (mt) cc_final: 0.7715 (mt) REVERT: 5 202 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8139 (mm-30) REVERT: 7 62 MET cc_start: 0.8513 (mtp) cc_final: 0.8050 (mtt) REVERT: 7 132 GLU cc_start: 0.7020 (tp30) cc_final: 0.6398 (tp30) REVERT: 9 53 GLU cc_start: 0.8484 (pt0) cc_final: 0.7906 (tm-30) REVERT: A 49 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: B 82 MET cc_start: 0.8683 (mmm) cc_final: 0.8255 (tpp) REVERT: B 283 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.6892 (mpt) REVERT: C 82 MET cc_start: 0.8788 (mmm) cc_final: 0.8520 (tpt) REVERT: D 326 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7702 (mtmm) REVERT: D 374 CYS cc_start: 0.7270 (m) cc_final: 0.7026 (m) REVERT: E 78 ASN cc_start: 0.7994 (t0) cc_final: 0.7649 (t0) REVERT: E 313 MET cc_start: 0.8503 (ttm) cc_final: 0.8179 (mtp) REVERT: G 16 MET cc_start: 0.8050 (mtp) cc_final: 0.7778 (mtt) REVERT: H 132 MET cc_start: 0.7603 (ttp) cc_final: 0.7336 (ttp) REVERT: J 305 MET cc_start: 0.9324 (mmm) cc_final: 0.9097 (tpp) REVERT: K 269 MET cc_start: 0.8547 (mmm) cc_final: 0.8313 (mmm) REVERT: N 67 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7277 (t-90) REVERT: N 81 ASP cc_start: 0.7439 (m-30) cc_final: 0.7149 (m-30) REVERT: N 84 ASP cc_start: 0.8201 (t0) cc_final: 0.7853 (t0) REVERT: N 125 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8170 (tm-30) REVERT: O 77 ASP cc_start: 0.7852 (t70) cc_final: 0.7544 (p0) REVERT: O 114 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: Q 61 THR cc_start: 0.8830 (m) cc_final: 0.8561 (m) REVERT: Q 117 ASP cc_start: 0.8262 (t0) cc_final: 0.7809 (t0) REVERT: Q 121 GLN cc_start: 0.8408 (tp40) cc_final: 0.8143 (tp40) REVERT: R 87 MET cc_start: 0.7432 (mmp) cc_final: 0.7227 (tpp) REVERT: R 117 ASP cc_start: 0.7886 (t70) cc_final: 0.7621 (t0) REVERT: R 121 GLN cc_start: 0.9342 (tm-30) cc_final: 0.8987 (tm-30) REVERT: S 41 GLU cc_start: 0.8128 (pt0) cc_final: 0.7876 (tm-30) REVERT: T 51 GLU cc_start: 0.7516 (mp0) cc_final: 0.7195 (mp0) REVERT: T 81 ASP cc_start: 0.7655 (m-30) cc_final: 0.7160 (m-30) REVERT: U 248 MET cc_start: -0.0352 (OUTLIER) cc_final: -0.0607 (ptt) REVERT: V 152 SER cc_start: 0.8526 (t) cc_final: 0.8192 (p) REVERT: Y 247 MET cc_start: 0.8811 (ttm) cc_final: 0.8573 (ttm) REVERT: Z 34 PHE cc_start: 0.8941 (p90) cc_final: 0.8407 (p90) REVERT: Z 35 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7376 (mt-10) REVERT: Z 84 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8302 (mm-30) outliers start: 85 outliers final: 73 residues processed: 640 average time/residue: 0.5571 time to fit residues: 626.7872 Evaluate side-chains 673 residues out of total 6573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 594 time to evaluate : 5.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 241 HIS Chi-restraints excluded: chain 1 residue 525 CYS Chi-restraints excluded: chain 2 residue 165 ILE Chi-restraints excluded: chain 2 residue 242 THR Chi-restraints excluded: chain 3 residue 135 CYS Chi-restraints excluded: chain 3 residue 241 TRP Chi-restraints excluded: chain 3 residue 523 VAL Chi-restraints excluded: chain 4 residue 202 PHE Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 287 LEU Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 304 TYR Chi-restraints excluded: chain 5 residue 123 THR Chi-restraints excluded: chain 6 residue 125 LEU Chi-restraints excluded: chain 6 residue 133 THR Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 9 residue 41 MET Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 107 GLU Chi-restraints excluded: chain J residue 119 MET Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 91 LEU Chi-restraints excluded: chain N residue 67 HIS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 92 LEU Chi-restraints excluded: chain O residue 71 VAL Chi-restraints excluded: chain O residue 72 SER Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 32 ASN Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 67 HIS Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 135 SER Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 154 VAL Chi-restraints excluded: chain U residue 226 HIS Chi-restraints excluded: chain U residue 248 MET Chi-restraints excluded: chain V residue 6 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 96 ASN Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain Y residue 210 ILE Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 746 random chunks: chunk 470 optimal weight: 1.9990 chunk 630 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 545 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 592 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 608 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 241 HIS 1 375 GLN ** 2 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN D 12 ASN G 12 ASN J 137 GLN ** R 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.079808 restraints weight = 137003.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081968 restraints weight = 67632.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082164 restraints weight = 44929.709| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 61482 Z= 0.485 Angle : 0.678 30.216 83150 Z= 0.333 Chirality : 0.045 0.271 9290 Planarity : 0.004 0.060 10688 Dihedral : 5.042 72.526 8390 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.33 % Allowed : 12.01 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 7524 helix: 1.92 (0.09), residues: 3687 sheet: 0.29 (0.18), residues: 888 loop : 0.23 (0.12), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 7 192 HIS 0.070 0.001 HIS 1 241 PHE 0.031 0.002 PHE Z 94 TYR 0.035 0.002 TYR 6 41 ARG 0.008 0.001 ARG C 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11446.38 seconds wall clock time: 200 minutes 38.98 seconds (12038.98 seconds total)