Starting phenix.real_space_refine on Tue Sep 24 17:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/09_2024/7t3l_25662.cif" } resolution = 3.6 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= 0.005 sd= 0.048 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 198 5.49 5 S 58 5.16 5 C 32169 2.51 5 N 9520 2.21 5 O 10274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 52219 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "J" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "K" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1766 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 16, 'TRANS': 211} Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3145 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 196 Chain: "b" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "c" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "d" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "e" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "f" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "g" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "h" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "i" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "m" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "O" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 462 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "P" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 399 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "R" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "Q" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 171 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 23.60, per 1000 atoms: 0.45 Number of scatterers: 52219 At special positions: 0 Unit cell: (156.45, 161.7, 236.25, 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 58 16.00 P 198 15.00 O 10274 8.00 N 9520 7.00 C 32169 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: 9.48 Conformation dependent library (CDL) restraints added in 5.1 seconds 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11608 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 103 sheets defined 34.6% alpha, 20.6% beta 49 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 15.15 Creating SS restraints... Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.945A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.506A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.519A pdb=" N ASP A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.773A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.729A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU B 118 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.901A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.598A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.991A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 74 through 77 removed outlier: 3.528A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.838A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA D 154 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 322 through 332 removed outlier: 3.521A pdb=" N LEU D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 51 through 55 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 208 through 223 Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY E 305 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER E 306 " --> pdb=" O PRO E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.532A pdb=" N LEU E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 208 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG I 169 " --> pdb=" O PHE I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 302 through 304 No H-bonds generated for 'chain 'I' and resid 302 through 304' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.523A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 136 Processing helix chain 'J' and resid 140 through 147 removed outlier: 3.753A pdb=" N ILE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 147 " --> pdb=" O THR J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.537A pdb=" N VAL J 151 " --> pdb=" O PRO J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 169 Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 191 through 200 Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'K' and resid 47 through 70 removed outlier: 4.201A pdb=" N ASP K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 136 Processing helix chain 'K' and resid 142 through 147 removed outlier: 3.873A pdb=" N LEU K 146 " --> pdb=" O TRP K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 191 through 200 Processing helix chain 'K' and resid 211 through 222 Processing helix chain 'a' and resid 9 through 33 removed outlier: 3.944A pdb=" N LEU a 13 " --> pdb=" O THR a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 45 Processing helix chain 'a' and resid 49 through 58 removed outlier: 4.128A pdb=" N LEU a 53 " --> pdb=" O ARG a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 100 Processing helix chain 'a' and resid 115 through 121 removed outlier: 3.899A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 135 Processing helix chain 'a' and resid 148 through 161 Processing helix chain 'a' and resid 195 through 212 Processing helix chain 'a' and resid 212 through 224 Processing helix chain 'a' and resid 247 through 251 Processing helix chain 'a' and resid 253 through 258 Processing helix chain 'a' and resid 285 through 290 Processing helix chain 'a' and resid 294 through 309 removed outlier: 3.910A pdb=" N ALA a 309 " --> pdb=" O GLN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 314 through 340 removed outlier: 3.504A pdb=" N ILE a 329 " --> pdb=" O LEU a 325 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 346 through 350 Processing helix chain 'a' and resid 359 through 364 removed outlier: 3.520A pdb=" N ASP a 364 " --> pdb=" O GLN a 360 " (cutoff:3.500A) Processing helix chain 'a' and resid 366 through 371 Processing helix chain 'a' and resid 375 through 383 removed outlier: 3.774A pdb=" N LEU a 379 " --> pdb=" O LEU a 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG a 380 " --> pdb=" O GLN a 376 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 397 Processing helix chain 'a' and resid 402 through 408 removed outlier: 3.687A pdb=" N LEU a 406 " --> pdb=" O ASP a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 431 removed outlier: 3.728A pdb=" N ASP a 431 " --> pdb=" O GLU a 427 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 48 removed outlier: 3.744A pdb=" N PHE b 37 " --> pdb=" O SER b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 120 removed outlier: 3.536A pdb=" N LEU b 118 " --> pdb=" O GLY b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 135 Processing helix chain 'b' and resid 165 through 180 Processing helix chain 'b' and resid 189 through 204 Processing helix chain 'b' and resid 208 through 216 Processing helix chain 'b' and resid 291 through 295 removed outlier: 3.901A pdb=" N VAL b 295 " --> pdb=" O PRO b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 302 removed outlier: 3.598A pdb=" N LEU b 302 " --> pdb=" O SER b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 312 removed outlier: 3.899A pdb=" N GLY b 312 " --> pdb=" O PRO b 309 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 36 removed outlier: 3.991A pdb=" N LEU c 20 " --> pdb=" O PRO c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 73 Processing helix chain 'c' and resid 74 through 77 removed outlier: 3.529A pdb=" N GLU c 77 " --> pdb=" O PRO c 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 74 through 77' Processing helix chain 'c' and resid 108 through 121 removed outlier: 3.730A pdb=" N LEU c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG c 118 " --> pdb=" O ARG c 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 131 Processing helix chain 'c' and resid 132 through 136 removed outlier: 3.836A pdb=" N VAL c 135 " --> pdb=" O PRO c 132 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA c 136 " --> pdb=" O ASP c 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 132 through 136' Processing helix chain 'd' and resid 51 through 55 Processing helix chain 'd' and resid 130 through 148 Processing helix chain 'd' and resid 150 through 163 removed outlier: 3.610A pdb=" N ALA d 154 " --> pdb=" O PHE d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 224 Processing helix chain 'd' and resid 275 through 284 removed outlier: 3.511A pdb=" N ILE d 279 " --> pdb=" O HIS d 275 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 304 No H-bonds generated for 'chain 'd' and resid 302 through 304' Processing helix chain 'd' and resid 322 through 332 removed outlier: 3.520A pdb=" N LEU d 332 " --> pdb=" O ASP d 328 " (cutoff:3.500A) Processing helix chain 'd' and resid 338 through 352 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 82 through 91 Processing helix chain 'e' and resid 130 through 148 Processing helix chain 'e' and resid 151 through 163 Processing helix chain 'e' and resid 208 through 223 Processing helix chain 'e' and resid 275 through 284 Processing helix chain 'e' and resid 302 through 306 removed outlier: 3.530A pdb=" N GLY e 305 " --> pdb=" O GLU e 302 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER e 306 " --> pdb=" O PRO e 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 302 through 306' Processing helix chain 'e' and resid 322 through 332 removed outlier: 3.533A pdb=" N LEU e 326 " --> pdb=" O ASP e 322 " (cutoff:3.500A) Processing helix chain 'e' and resid 338 through 352 Processing helix chain 'f' and resid 51 through 55 removed outlier: 3.796A pdb=" N SER f 55 " --> pdb=" O ARG f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 91 Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 151 through 163 Processing helix chain 'f' and resid 208 through 223 Processing helix chain 'f' and resid 275 through 284 Processing helix chain 'f' and resid 302 through 304 No H-bonds generated for 'chain 'f' and resid 302 through 304' Processing helix chain 'f' and resid 322 through 332 Processing helix chain 'f' and resid 338 through 352 Processing helix chain 'g' and resid 82 through 92 Processing helix chain 'g' and resid 130 through 148 Processing helix chain 'g' and resid 151 through 163 Processing helix chain 'g' and resid 208 through 223 Processing helix chain 'g' and resid 275 through 284 Processing helix chain 'g' and resid 322 through 332 Processing helix chain 'g' and resid 338 through 352 Processing helix chain 'h' and resid 82 through 92 Processing helix chain 'h' and resid 130 through 148 Processing helix chain 'h' and resid 151 through 163 Processing helix chain 'h' and resid 208 through 223 Processing helix chain 'h' and resid 275 through 284 Processing helix chain 'h' and resid 302 through 304 No H-bonds generated for 'chain 'h' and resid 302 through 304' Processing helix chain 'h' and resid 322 through 331 Processing helix chain 'h' and resid 338 through 352 Processing helix chain 'i' and resid 82 through 92 Processing helix chain 'i' and resid 130 through 148 Processing helix chain 'i' and resid 150 through 163 Processing helix chain 'i' and resid 164 through 171 removed outlier: 6.331A pdb=" N ARG i 169 " --> pdb=" O PHE i 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 208 through 224 Processing helix chain 'i' and resid 275 through 284 Processing helix chain 'i' and resid 302 through 304 No H-bonds generated for 'chain 'i' and resid 302 through 304' Processing helix chain 'i' and resid 322 through 332 Processing helix chain 'i' and resid 338 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 5.658A pdb=" N GLY B 285 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY B 287 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN B 220 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB6, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.880A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 177 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP D 196 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL D 179 " --> pdb=" O ARG D 194 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 194 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 181 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA D 192 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS D 183 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC3, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.576A pdb=" N LYS D 312 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.807A pdb=" N PHE E 355 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.828A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG E 194 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'E' and resid 63 through 70 removed outlier: 4.514A pdb=" N ALA E 101 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 32 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.911A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 177 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASP F 196 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL F 179 " --> pdb=" O ARG F 194 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG F 194 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AD3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AD4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD5, first strand: chain 'F' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS F 312 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AD7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE H 355 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 188 through 196 removed outlier: 6.471A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG H 194 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL H 179 " --> pdb=" O ARG H 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP H 196 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS H 261 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR H 97 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS H 263 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 265 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA H 101 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AE7, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL H 307 " --> pdb=" O LYS H 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.698A pdb=" N GLY I 353 " --> pdb=" O PHE I 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL I 177 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP I 196 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 179 " --> pdb=" O ARG I 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG I 194 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG I 117 " --> pdb=" O ASP I 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.945A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 243 through 244 removed outlier: 4.575A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR J 12 " --> pdb=" O TYR J 31 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR J 31 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA J 14 " --> pdb=" O THR J 29 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR J 29 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG J 16 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN J 27 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS J 26 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR J 41 " --> pdb=" O HIS J 26 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP J 28 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 39 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU J 30 " --> pdb=" O MET J 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF5, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.525A pdb=" N VAL I 307 " --> pdb=" O LYS I 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 85 through 91 removed outlier: 3.602A pdb=" N ASP J 73 " --> pdb=" O VAL J 91 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU J 119 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER J 99 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 6 removed outlier: 4.221A pdb=" N ALA K 38 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TYR K 32 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU K 36 " --> pdb=" O TYR K 32 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 19 through 20 removed outlier: 5.783A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR i 97 " --> pdb=" O HIS K 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN i 94 " --> pdb=" O GLY i 70 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 19 through 20 removed outlier: 5.783A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR i 97 " --> pdb=" O HIS K 19 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA i 101 " --> pdb=" O VAL i 244 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 85 through 90 removed outlier: 5.362A pdb=" N LEU K 119 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 64 through 66 Processing sheet with id=AG3, first strand: chain 'a' and resid 94 through 95 Processing sheet with id=AG4, first strand: chain 'a' and resid 94 through 95 removed outlier: 5.659A pdb=" N GLY b 285 " --> pdb=" O PRO b 252 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY b 287 " --> pdb=" O PRO b 250 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA b 253 " --> pdb=" O TRP b 316 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP b 316 " --> pdb=" O ALA b 253 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 180 through 181 Processing sheet with id=AG6, first strand: chain 'a' and resid 239 through 240 removed outlier: 4.221A pdb=" N PHE b 81 " --> pdb=" O ILE a 240 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 265 through 267 removed outlier: 5.780A pdb=" N LEU a 265 " --> pdb=" O TRP b 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'b' and resid 55 through 61 removed outlier: 3.891A pdb=" N VAL b 59 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU b 110 " --> pdb=" O VAL b 59 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE b 61 " --> pdb=" O SER b 108 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER b 108 " --> pdb=" O ILE b 61 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU b 105 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN b 18 " --> pdb=" O LEU b 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL b 107 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER b 16 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU b 109 " --> pdb=" O ARG b 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG b 14 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU b 111 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU b 12 " --> pdb=" O LEU b 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL b 113 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU b 10 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER b 16 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 65 through 68 removed outlier: 4.821A pdb=" N LEU b 105 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN b 18 " --> pdb=" O LEU b 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL b 107 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N SER b 16 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU b 109 " --> pdb=" O ARG b 14 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ARG b 14 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU b 111 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU b 12 " --> pdb=" O LEU b 111 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL b 113 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU b 10 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 220 through 222 removed outlier: 4.696A pdb=" N ASN b 220 " --> pdb=" O ARG b 242 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 41 through 43 Processing sheet with id=AH3, first strand: chain 'c' and resid 41 through 43 Processing sheet with id=AH4, first strand: chain 'c' and resid 97 through 98 Processing sheet with id=AH5, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AH6, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AH7, first strand: chain 'd' and resid 38 through 39 removed outlier: 3.879A pdb=" N VAL d 228 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU d 229 " --> pdb=" O ILE d 184 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL d 177 " --> pdb=" O ASP d 196 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP d 196 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL d 179 " --> pdb=" O ARG d 194 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG d 194 " --> pdb=" O VAL d 179 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE d 181 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA d 192 " --> pdb=" O ILE d 181 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS d 183 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 42 through 43 Processing sheet with id=AH9, first strand: chain 'd' and resid 46 through 47 Processing sheet with id=AI1, first strand: chain 'd' and resid 64 through 66 Processing sheet with id=AI2, first strand: chain 'd' and resid 248 through 249 removed outlier: 3.771A pdb=" N THR d 264 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 285 through 287 Processing sheet with id=AI4, first strand: chain 'd' and resid 306 through 307 removed outlier: 3.575A pdb=" N LYS d 312 " --> pdb=" O VAL d 307 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 127 through 128 removed outlier: 3.806A pdb=" N PHE e 355 " --> pdb=" O LEU e 31 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'e' and resid 38 through 39 removed outlier: 3.827A pdb=" N VAL e 228 " --> pdb=" O VAL e 118 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU e 229 " --> pdb=" O ILE e 184 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL e 179 " --> pdb=" O ARG e 194 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG e 194 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE e 181 " --> pdb=" O ALA e 192 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA e 192 " --> pdb=" O ILE e 181 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS e 183 " --> pdb=" O ALA e 190 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'e' and resid 38 through 39 Processing sheet with id=AI8, first strand: chain 'e' and resid 63 through 70 removed outlier: 4.513A pdb=" N ALA e 101 " --> pdb=" O VAL e 244 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'e' and resid 285 through 287 Processing sheet with id=AJ1, first strand: chain 'f' and resid 31 through 32 Processing sheet with id=AJ2, first strand: chain 'f' and resid 38 through 39 removed outlier: 3.912A pdb=" N VAL f 228 " --> pdb=" O VAL f 118 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU f 229 " --> pdb=" O ILE f 184 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL f 177 " --> pdb=" O ASP f 196 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP f 196 " --> pdb=" O VAL f 177 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL f 179 " --> pdb=" O ARG f 194 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG f 194 " --> pdb=" O VAL f 179 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE f 181 " --> pdb=" O ALA f 192 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA f 192 " --> pdb=" O ILE f 181 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS f 183 " --> pdb=" O ALA f 190 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 38 through 39 Processing sheet with id=AJ4, first strand: chain 'f' and resid 64 through 70 Processing sheet with id=AJ5, first strand: chain 'f' and resid 285 through 287 Processing sheet with id=AJ6, first strand: chain 'f' and resid 306 through 307 removed outlier: 3.672A pdb=" N LYS f 312 " --> pdb=" O VAL f 307 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'g' and resid 31 through 33 Processing sheet with id=AJ8, first strand: chain 'g' and resid 38 through 39 removed outlier: 3.899A pdb=" N VAL g 228 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU g 229 " --> pdb=" O ILE g 184 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL g 177 " --> pdb=" O ASP g 196 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP g 196 " --> pdb=" O VAL g 177 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL g 179 " --> pdb=" O ARG g 194 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG g 194 " --> pdb=" O VAL g 179 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE g 181 " --> pdb=" O ALA g 192 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA g 192 " --> pdb=" O ILE g 181 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS g 183 " --> pdb=" O ALA g 190 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'g' and resid 38 through 39 Processing sheet with id=AK1, first strand: chain 'g' and resid 63 through 70 removed outlier: 4.377A pdb=" N ALA g 101 " --> pdb=" O VAL g 244 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'g' and resid 285 through 287 Processing sheet with id=AK3, first strand: chain 'h' and resid 127 through 128 removed outlier: 3.983A pdb=" N PHE h 355 " --> pdb=" O LEU h 31 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'h' and resid 188 through 196 removed outlier: 6.472A pdb=" N HIS h 183 " --> pdb=" O ALA h 190 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA h 192 " --> pdb=" O ILE h 181 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE h 181 " --> pdb=" O ALA h 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG h 194 " --> pdb=" O VAL h 179 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL h 179 " --> pdb=" O ARG h 194 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP h 196 " --> pdb=" O VAL h 177 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL h 177 " --> pdb=" O ASP h 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU h 229 " --> pdb=" O ILE h 184 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL h 228 " --> pdb=" O VAL h 118 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA h 101 " --> pdb=" O VAL h 244 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'h' and resid 63 through 70 removed outlier: 3.824A pdb=" N ASN h 94 " --> pdb=" O GLY h 70 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS h 261 " --> pdb=" O LEU h 95 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR h 97 " --> pdb=" O LYS h 261 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS h 263 " --> pdb=" O THR h 97 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU h 265 " --> pdb=" O ASP h 99 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA h 101 " --> pdb=" O LEU h 265 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR h 264 " --> pdb=" O GLU h 249 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'h' and resid 285 through 287 Processing sheet with id=AK8, first strand: chain 'h' and resid 306 through 307 removed outlier: 3.944A pdb=" N VAL h 307 " --> pdb=" O LYS h 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS h 312 " --> pdb=" O VAL h 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'i' and resid 127 through 128 removed outlier: 3.699A pdb=" N GLY i 353 " --> pdb=" O PHE i 33 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'i' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG i 117 " --> pdb=" O ASP i 38 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU i 229 " --> pdb=" O ILE i 184 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL i 177 " --> pdb=" O ASP i 196 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP i 196 " --> pdb=" O VAL i 177 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL i 179 " --> pdb=" O ARG i 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARG i 194 " --> pdb=" O VAL i 179 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE i 181 " --> pdb=" O ALA i 192 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA i 192 " --> pdb=" O ILE i 181 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS i 183 " --> pdb=" O ALA i 190 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'i' and resid 38 through 39 removed outlier: 3.523A pdb=" N ARG i 117 " --> pdb=" O ASP i 38 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'i' and resid 285 through 287 Processing sheet with id=AL4, first strand: chain 'i' and resid 306 through 307 removed outlier: 3.525A pdb=" N VAL i 307 " --> pdb=" O LYS i 312 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS i 312 " --> pdb=" O VAL i 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 2101 hydrogen bonds defined for protein. 5754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 133 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 18.71 Time building geometry restraints manager: 11.37 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: 10159 1.33 - 1.45: 13887 1.45 - 1.57: 29180 1.57 - 1.69: 392 1.69 - 1.81: 90 Bond restraints: 53708 Sorted by residual: bond pdb=" C ARG K 116 " pdb=" O ARG K 116 " ideal model delta sigma weight residual 1.244 1.205 0.038 9.40e-03 1.13e+04 1.67e+01 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C LEU b 181 " pdb=" N PRO b 182 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" N ARG K 116 " pdb=" CA ARG K 116 " ideal model delta sigma weight residual 1.462 1.448 0.014 7.70e-03 1.69e+04 3.13e+00 bond pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 1.525 1.503 0.022 1.29e-02 6.01e+03 2.96e+00 ... (remaining 53703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 72584 2.44 - 4.88: 1090 4.88 - 7.32: 154 7.32 - 9.76: 35 9.76 - 12.20: 4 Bond angle restraints: 73867 Sorted by residual: angle pdb=" N ASN a 256 " pdb=" CA ASN a 256 " pdb=" C ASN a 256 " ideal model delta sigma weight residual 112.90 104.71 8.19 1.31e+00 5.83e-01 3.91e+01 angle pdb=" C ASP K 202 " pdb=" CA ASP K 202 " pdb=" CB ASP K 202 " ideal model delta sigma weight residual 116.54 109.56 6.98 1.15e+00 7.56e-01 3.68e+01 angle pdb=" C ASP J 202 " pdb=" CA ASP J 202 " pdb=" CB ASP J 202 " ideal model delta sigma weight residual 116.54 109.85 6.69 1.15e+00 7.56e-01 3.39e+01 angle pdb=" N SER K 92 " pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 112.04 105.11 6.93 1.44e+00 4.82e-01 2.32e+01 angle pdb=" N PRO K 34 " pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 114.68 109.80 4.88 1.04e+00 9.25e-01 2.20e+01 ... (remaining 73862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 30692 35.77 - 71.54: 1286 71.54 - 107.32: 78 107.32 - 143.09: 2 143.09 - 178.86: 12 Dihedral angle restraints: 32070 sinusoidal: 14094 harmonic: 17976 Sorted by residual: dihedral pdb=" O4' U m 33 " pdb=" C1' U m 33 " pdb=" N1 U m 33 " pdb=" C2 U m 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.34 147.66 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 52.48 147.52 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U m 21 " pdb=" C1' U m 21 " pdb=" N1 U m 21 " pdb=" C2 U m 21 " ideal model delta sinusoidal sigma weight residual 200.00 52.65 147.35 1 1.50e+01 4.44e-03 7.86e+01 ... (remaining 32067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 7241 0.065 - 0.131: 993 0.131 - 0.196: 70 0.196 - 0.262: 15 0.262 - 0.327: 5 Chirality restraints: 8324 Sorted by residual: chirality pdb=" CB ILE E 72 " pdb=" CA ILE E 72 " pdb=" CG1 ILE E 72 " pdb=" CG2 ILE E 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE e 72 " pdb=" CA ILE e 72 " pdb=" CG1 ILE e 72 " pdb=" CG2 ILE e 72 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE K 6 " pdb=" CA ILE K 6 " pdb=" CG1 ILE K 6 " pdb=" CG2 ILE K 6 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 8321 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 82 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.60e+01 pdb=" N PRO F 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO F 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP f 82 " 0.085 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO f 83 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO f 83 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO f 83 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 72 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.045 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6999 2.76 - 3.29: 48185 3.29 - 3.83: 95277 3.83 - 4.36: 114069 4.36 - 4.90: 186402 Nonbonded interactions: 450932 Sorted by model distance: nonbonded pdb=" CD2 LEU K 119 " pdb=" OE1 GLN g 91 " model vdw 2.223 3.460 nonbonded pdb=" OH TYR g 290 " pdb=" O GLY g 297 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.243 3.040 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.281 3.040 ... (remaining 450927 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 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 1 through 174 or resid 176 through 187)) selection = (chain 'c' and (resid 1 through 174 or resid 176 through 187)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = chain 'd' selection = (chain 'e' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'f' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'g' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'h' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'i' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } ncs_group { reference = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'R' selection = chain 'S' } 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=0.00 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: 0.810 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: 0.040 Extract box with map and model: 1.590 Check model and map are aligned: 0.320 Set scattering table: 0.370 Process input model: 100.290 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 53708 Z= 0.242 Angle : 0.743 12.202 73867 Z= 0.406 Chirality : 0.046 0.327 8324 Planarity : 0.007 0.127 9006 Dihedral : 18.087 178.858 20462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 0.52 % Allowed : 17.31 % Favored : 82.17 % 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: -1.92 (0.09), residues: 6192 helix: -1.26 (0.09), residues: 1958 sheet: 0.41 (0.17), residues: 966 loop : -1.83 (0.10), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 193 HIS 0.008 0.001 HIS D 159 PHE 0.015 0.002 PHE K 212 TYR 0.045 0.002 TYR D 304 ARG 0.014 0.001 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 315 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 MET cc_start: 0.6486 (mmt) cc_final: 0.6213 (mmt) REVERT: K 6 ILE cc_start: 0.9050 (tp) cc_final: 0.8665 (mp) REVERT: g 82 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.4438 (t0) outliers start: 25 outliers final: 3 residues processed: 340 average time/residue: 0.5553 time to fit residues: 311.2619 Evaluate side-chains 152 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 4.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain g residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 530 optimal weight: 9.9990 chunk 475 optimal weight: 0.8980 chunk 264 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 254 optimal weight: 0.0870 chunk 492 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 366 optimal weight: 6.9990 chunk 570 optimal weight: 20.0000 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 146 ASN D 183 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN F 91 GLN F 160 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN H 343 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN K 169 HIS K 194 ASN a 64 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 GLN ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 148 GLN e 160 ASN ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 ASN g 242 GLN h 343 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4875 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 53708 Z= 0.175 Angle : 0.582 14.211 73867 Z= 0.300 Chirality : 0.040 0.208 8324 Planarity : 0.005 0.073 9006 Dihedral : 17.398 179.935 9476 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.59 % Allowed : 17.54 % Favored : 80.87 % 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: -0.77 (0.10), residues: 6192 helix: 0.39 (0.11), residues: 1968 sheet: 0.74 (0.17), residues: 924 loop : -1.49 (0.10), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP b 29 HIS 0.022 0.001 HIS K 68 PHE 0.021 0.001 PHE J 195 TYR 0.023 0.001 TYR K 32 ARG 0.007 0.000 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 157 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.6438 (OUTLIER) cc_final: 0.6138 (m) REVERT: H 78 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7502 (p) outliers start: 77 outliers final: 19 residues processed: 226 average time/residue: 0.5327 time to fit residues: 206.4147 Evaluate side-chains 146 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain a residue 216 LYS Chi-restraints excluded: chain a residue 387 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain g residue 82 ASP Chi-restraints excluded: chain g residue 116 LEU Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain i residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 474 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 571 optimal weight: 5.9990 chunk 617 optimal weight: 20.0000 chunk 508 optimal weight: 0.0040 chunk 566 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 458 optimal weight: 20.0000 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS D 183 HIS D 319 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 260 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN J 25 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 319 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 260 GLN e 348 ASN ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 183 HIS i 348 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 53708 Z= 0.196 Angle : 0.570 14.208 73867 Z= 0.292 Chirality : 0.038 0.226 8324 Planarity : 0.004 0.061 9006 Dihedral : 17.339 177.514 9476 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.57 % Allowed : 17.27 % Favored : 81.16 % 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: -0.27 (0.11), residues: 6192 helix: 1.11 (0.11), residues: 1970 sheet: 0.72 (0.17), residues: 992 loop : -1.35 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 228 HIS 0.013 0.001 HIS K 68 PHE 0.019 0.001 PHE K 195 TYR 0.032 0.002 TYR K 198 ARG 0.021 0.000 ARG d 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 130 time to evaluate : 4.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.6188 (OUTLIER) cc_final: 0.5870 (m) outliers start: 76 outliers final: 21 residues processed: 198 average time/residue: 0.5074 time to fit residues: 176.7139 Evaluate side-chains 139 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain a residue 422 LEU Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain f residue 44 MET Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 564 optimal weight: 4.9990 chunk 429 optimal weight: 20.0000 chunk 296 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 272 optimal weight: 50.0000 chunk 383 optimal weight: 0.8980 chunk 573 optimal weight: 50.0000 chunk 607 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 543 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 53708 Z= 0.143 Angle : 0.539 14.556 73867 Z= 0.274 Chirality : 0.038 0.285 8324 Planarity : 0.004 0.061 9006 Dihedral : 17.337 177.167 9474 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.63 % Allowed : 17.15 % Favored : 81.22 % 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: -0.08 (0.11), residues: 6192 helix: 1.38 (0.11), residues: 1984 sheet: 0.80 (0.17), residues: 958 loop : -1.29 (0.11), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 193 HIS 0.011 0.001 HIS K 68 PHE 0.017 0.001 PHE K 195 TYR 0.022 0.001 TYR E 133 ARG 0.005 0.000 ARG d 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 124 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.6311 (OUTLIER) cc_final: 0.5963 (m) REVERT: F 250 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4850 (tt) REVERT: H 78 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7434 (p) REVERT: g 44 MET cc_start: 0.3919 (mpp) cc_final: 0.3669 (ptp) outliers start: 79 outliers final: 29 residues processed: 196 average time/residue: 0.4934 time to fit residues: 169.8393 Evaluate side-chains 147 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain i residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 9.9990 chunk 344 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 451 optimal weight: 30.0000 chunk 250 optimal weight: 6.9990 chunk 518 optimal weight: 20.0000 chunk 419 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 309 optimal weight: 20.0000 chunk 544 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 348 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN H 183 HIS ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 253 GLN ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN b 131 GLN ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 102 ASN e 186 GLN ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 96 GLN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 342 GLN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 ASN h 348 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 53708 Z= 0.367 Angle : 0.757 14.777 73867 Z= 0.390 Chirality : 0.042 0.583 8324 Planarity : 0.006 0.070 9006 Dihedral : 17.513 175.670 9474 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.16 % Allowed : 17.52 % Favored : 80.32 % 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: -0.36 (0.11), residues: 6192 helix: 0.85 (0.11), residues: 2004 sheet: 0.64 (0.16), residues: 1006 loop : -1.28 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP e 193 HIS 0.012 0.002 HIS K 169 PHE 0.077 0.002 PHE a 232 TYR 0.039 0.003 TYR f 157 ARG 0.032 0.001 ARG J 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 99 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 MET cc_start: 0.3665 (tpt) cc_final: 0.3386 (tpt) REVERT: B 24 SER cc_start: 0.5909 (OUTLIER) cc_final: 0.5588 (m) REVERT: C 56 GLU cc_start: 0.6190 (tm-30) cc_final: 0.5945 (pp20) outliers start: 105 outliers final: 62 residues processed: 198 average time/residue: 0.5249 time to fit residues: 178.3677 Evaluate side-chains 153 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 90 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 147 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 68 HIS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain a residue 70 LEU Chi-restraints excluded: chain a residue 387 VAL Chi-restraints excluded: chain a residue 420 LYS Chi-restraints excluded: chain a residue 422 LEU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 72 GLN Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain d residue 250 LEU Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain e residue 51 GLN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 10.0000 chunk 546 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 607 optimal weight: 9.9990 chunk 504 optimal weight: 30.0000 chunk 281 optimal weight: 30.0000 chunk 50 optimal weight: 40.0000 chunk 200 optimal weight: 30.0000 chunk 318 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 289 HIS ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 342 GLN h 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 53708 Z= 0.161 Angle : 0.562 17.727 73867 Z= 0.285 Chirality : 0.038 0.382 8324 Planarity : 0.004 0.060 9006 Dihedral : 17.433 176.698 9472 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.63 % Allowed : 18.34 % Favored : 80.03 % 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: -0.01 (0.11), residues: 6192 helix: 1.37 (0.11), residues: 2016 sheet: 0.64 (0.16), residues: 996 loop : -1.17 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 347 HIS 0.012 0.001 HIS K 68 PHE 0.016 0.001 PHE K 62 TYR 0.032 0.002 TYR G 157 ARG 0.012 0.000 ARG a 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 111 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.5993 (OUTLIER) cc_final: 0.5677 (m) REVERT: c 1 MET cc_start: 0.1966 (tpt) cc_final: 0.1584 (mmm) outliers start: 79 outliers final: 44 residues processed: 185 average time/residue: 0.5308 time to fit residues: 168.6124 Evaluate side-chains 150 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 105 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 51 GLN Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 422 LEU Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 72 GLN Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain f residue 270 ASP Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain i residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 585 optimal weight: 50.0000 chunk 68 optimal weight: 30.0000 chunk 346 optimal weight: 6.9990 chunk 443 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 chunk 511 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 605 optimal weight: 4.9990 chunk 378 optimal weight: 7.9990 chunk 369 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN I 348 ASN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 227 HIS ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 53708 Z= 0.187 Angle : 0.565 12.275 73867 Z= 0.288 Chirality : 0.038 0.370 8324 Planarity : 0.004 0.059 9006 Dihedral : 17.323 177.353 9472 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.33 % Favored : 94.65 % Rotamer: Outliers : 1.48 % Allowed : 18.67 % Favored : 79.84 % 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: 0.11 (0.11), residues: 6192 helix: 1.57 (0.12), residues: 2000 sheet: 0.60 (0.16), residues: 996 loop : -1.11 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 29 HIS 0.011 0.001 HIS K 68 PHE 0.013 0.001 PHE K 195 TYR 0.023 0.001 TYR J 128 ARG 0.011 0.000 ARG f 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 104 time to evaluate : 4.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.5949 (OUTLIER) cc_final: 0.5618 (m) REVERT: c 1 MET cc_start: 0.1901 (tpt) cc_final: 0.1492 (mmm) outliers start: 72 outliers final: 52 residues processed: 173 average time/residue: 0.5442 time to fit residues: 161.6980 Evaluate side-chains 150 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 97 time to evaluate : 4.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 70 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 422 LEU Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 72 GLN Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain f residue 270 ASP Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain i residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 374 optimal weight: 20.0000 chunk 241 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 118 optimal weight: 50.0000 chunk 117 optimal weight: 10.0000 chunk 384 optimal weight: 20.0000 chunk 412 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 475 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5341 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 53708 Z= 0.193 Angle : 0.567 12.406 73867 Z= 0.288 Chirality : 0.038 0.373 8324 Planarity : 0.004 0.058 9006 Dihedral : 17.320 179.062 9472 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.53 % Allowed : 18.51 % Favored : 79.97 % 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: 0.16 (0.11), residues: 6192 helix: 1.60 (0.12), residues: 2004 sheet: 0.58 (0.16), residues: 996 loop : -1.06 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 29 HIS 0.011 0.001 HIS K 68 PHE 0.024 0.001 PHE K 62 TYR 0.031 0.001 TYR J 109 ARG 0.007 0.000 ARG b 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 93 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.5871 (OUTLIER) cc_final: 0.5526 (m) REVERT: c 1 MET cc_start: 0.2014 (tpt) cc_final: 0.1665 (mmm) outliers start: 74 outliers final: 58 residues processed: 159 average time/residue: 0.5349 time to fit residues: 145.8781 Evaluate side-chains 152 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 93 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 281 MET Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 72 GLN Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain d residue 270 ASP Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain f residue 270 ASP Chi-restraints excluded: chain f residue 327 LEU Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 256 ASP Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain i residue 355 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 550 optimal weight: 6.9990 chunk 579 optimal weight: 0.0980 chunk 529 optimal weight: 7.9990 chunk 564 optimal weight: 4.9990 chunk 339 optimal weight: 6.9990 chunk 245 optimal weight: 3.9990 chunk 442 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 509 optimal weight: 9.9990 chunk 533 optimal weight: 0.6980 chunk 562 optimal weight: 50.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 53708 Z= 0.144 Angle : 0.545 12.975 73867 Z= 0.275 Chirality : 0.038 0.342 8324 Planarity : 0.004 0.063 9006 Dihedral : 17.236 178.250 9472 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.01 % Allowed : 19.00 % Favored : 79.99 % 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: 0.21 (0.11), residues: 6192 helix: 1.68 (0.12), residues: 1992 sheet: 0.68 (0.16), residues: 970 loop : -1.06 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 29 HIS 0.012 0.001 HIS K 68 PHE 0.015 0.001 PHE J 9 TYR 0.024 0.001 TYR J 128 ARG 0.008 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 100 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.5827 (OUTLIER) cc_final: 0.5485 (m) REVERT: c 1 MET cc_start: 0.2077 (tpt) cc_final: 0.1652 (mmm) outliers start: 49 outliers final: 41 residues processed: 146 average time/residue: 0.5077 time to fit residues: 130.3717 Evaluate side-chains 139 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 97 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 281 MET Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain i residue 355 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 370 optimal weight: 40.0000 chunk 596 optimal weight: 5.9990 chunk 364 optimal weight: 50.0000 chunk 282 optimal weight: 30.0000 chunk 414 optimal weight: 8.9990 chunk 625 optimal weight: 80.0000 chunk 575 optimal weight: 10.0000 chunk 498 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 384 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5334 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 53708 Z= 0.173 Angle : 0.551 13.003 73867 Z= 0.279 Chirality : 0.038 0.329 8324 Planarity : 0.004 0.062 9006 Dihedral : 17.189 179.561 9472 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.01 % Allowed : 19.08 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 6192 helix: 1.72 (0.12), residues: 2000 sheet: 0.61 (0.16), residues: 994 loop : -1.05 (0.11), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 29 HIS 0.012 0.001 HIS K 68 PHE 0.031 0.001 PHE K 195 TYR 0.028 0.001 TYR J 128 ARG 0.005 0.000 ARG D 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12384 Ramachandran restraints generated. 6192 Oldfield, 0 Emsley, 6192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 96 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 SER cc_start: 0.5849 (OUTLIER) cc_final: 0.5356 (m) REVERT: c 1 MET cc_start: 0.2259 (tpt) cc_final: 0.1896 (mmm) outliers start: 49 outliers final: 44 residues processed: 142 average time/residue: 0.5228 time to fit residues: 130.3757 Evaluate side-chains 139 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 281 MET Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain d residue 266 TYR Chi-restraints excluded: chain d residue 286 ILE Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain f residue 232 VAL Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 115 THR Chi-restraints excluded: chain i residue 355 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 395 optimal weight: 0.9990 chunk 530 optimal weight: 10.0000 chunk 152 optimal weight: 0.0570 chunk 459 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 498 optimal weight: 4.9990 chunk 208 optimal weight: 10.0000 chunk 512 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 HIS ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.035923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.023775 restraints weight = 824846.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.024221 restraints weight = 621799.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.024336 restraints weight = 463578.585| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 53708 Z= 0.142 Angle : 0.545 13.164 73867 Z= 0.272 Chirality : 0.038 0.310 8324 Planarity : 0.004 0.066 9006 Dihedral : 17.124 179.166 9472 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.91 % Allowed : 19.25 % Favored : 79.84 % 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: 0.23 (0.11), residues: 6192 helix: 1.70 (0.12), residues: 2000 sheet: 0.56 (0.16), residues: 1006 loop : -1.02 (0.11), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 29 HIS 0.011 0.001 HIS K 68 PHE 0.013 0.001 PHE K 62 TYR 0.026 0.001 TYR J 128 ARG 0.009 0.000 ARG e 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6752.50 seconds wall clock time: 121 minutes 1.08 seconds (7261.08 seconds total)