Starting phenix.real_space_refine on Tue Mar 26 00:27:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/03_2024/7t3l_25662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/03_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_25662/03_2024/7t3l_25662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/03_2024/7t3l_25662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/03_2024/7t3l_25662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3l_25662/03_2024/7t3l_25662.pdb" } 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 Residue "D GLU 34": "OE1" <-> "OE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 158": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "d GLU 34": "OE1" <-> "OE2" Residue "d PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "g GLU 302": "OE1" <-> "OE2" Residue "h GLU 57": "OE1" <-> "OE2" Residue "h GLU 188": "OE1" <-> "OE2" Residue "h TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 34": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 26.76, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.45 Conformation dependent library (CDL) restraints added in 9.3 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: 17.18 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: 22.03 Time building geometry restraints manager: 21.09 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: 93.98 - 102.23: 212 102.23 - 110.48: 15591 110.48 - 118.73: 28334 118.73 - 126.97: 28567 126.97 - 135.22: 1163 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 2.440 nonbonded pdb=" OH TYR G 290 " pdb=" O GLY G 297 " model vdw 2.243 2.440 nonbonded pdb=" O ALA J 141 " pdb=" OG1 THR J 144 " model vdw 2.266 2.440 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.281 2.440 ... (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 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: 1.220 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: 7.510 Check model and map are aligned: 0.750 Set scattering table: 0.460 Process input model: 142.170 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.940 ------------------------------------------------------------------------------- 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 : 5.415 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: 0.6635 time to fit residues: 372.3879 Evaluate side-chains 152 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 5.282 ------------------------------------------------------------------------------- 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: 0.4980 chunk 264 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 321 optimal weight: 3.9990 chunk 254 optimal weight: 0.0370 chunk 492 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 299 optimal weight: 0.7980 chunk 366 optimal weight: 8.9990 chunk 570 optimal weight: 7.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- 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 203 HIS ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS D 146 ASN D 183 HIS E 148 GLN F 91 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS K 194 ASN ** a 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 HIS d 183 HIS e 148 GLN f 129 ASN f 160 ASN ** h 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 53708 Z= 0.160 Angle : 0.569 14.691 73867 Z= 0.292 Chirality : 0.039 0.207 8324 Planarity : 0.004 0.073 9006 Dihedral : 17.375 179.838 9476 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.42 % Allowed : 18.76 % Favored : 79.82 % 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: -0.80 (0.10), residues: 6192 helix: 0.35 (0.11), residues: 1968 sheet: 0.78 (0.17), residues: 964 loop : -1.55 (0.10), residues: 3260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP b 29 HIS 0.017 0.001 HIS K 68 PHE 0.024 0.001 PHE K 62 TYR 0.025 0.001 TYR K 32 ARG 0.008 0.000 ARG b 77 *********************** 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 232 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 163 time to evaluate : 5.330 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: A 281 MET cc_start: 0.3100 (tpt) cc_final: 0.2894 (tpt) REVERT: K 1 MET cc_start: 0.8080 (tmm) cc_final: 0.7656 (tmm) outliers start: 69 outliers final: 16 residues processed: 221 average time/residue: 0.6222 time to fit residues: 235.9750 Evaluate side-chains 145 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP 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 J residue 46 TYR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 210 ILE Chi-restraints excluded: chain a residue 213 ASP Chi-restraints excluded: chain a residue 387 VAL Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain g residue 82 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 4.9990 chunk 176 optimal weight: 40.0000 chunk 474 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 571 optimal weight: 8.9990 chunk 617 optimal weight: 20.0000 chunk 508 optimal weight: 20.0000 chunk 566 optimal weight: 30.0000 chunk 194 optimal weight: 10.0000 chunk 458 optimal weight: 0.3980 overall best weight: 6.6788 ------------------------------------------------------------------------------- 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 72 GLN ** B 156 ASN ** 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 183 HIS D 319 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS H 242 GLN H 343 HIS ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 HIS d 319 GLN ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 348 ASN ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 183 HIS h 281 ASN ** h 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 348 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 53708 Z= 0.230 Angle : 0.604 13.921 73867 Z= 0.310 Chirality : 0.038 0.220 8324 Planarity : 0.004 0.060 9006 Dihedral : 17.289 177.760 9474 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.23 % Allowed : 17.56 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 6192 helix: 1.17 (0.11), residues: 1972 sheet: 0.83 (0.17), residues: 990 loop : -1.32 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 228 HIS 0.010 0.001 HIS K 68 PHE 0.018 0.002 PHE E 33 TYR 0.042 0.002 TYR K 198 ARG 0.022 0.001 ARG K 226 *********************** 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 232 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 124 time to evaluate : 5.311 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: F 250 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4727 (tt) REVERT: K 1 MET cc_start: 0.8357 (tmm) cc_final: 0.7671 (tmm) REVERT: K 62 PHE cc_start: 0.8363 (t80) cc_final: 0.8067 (t80) outliers start: 108 outliers final: 42 residues processed: 222 average time/residue: 0.6016 time to fit residues: 235.5455 Evaluate side-chains 145 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 147 ASP Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain J residue 207 ARG Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 213 ASP Chi-restraints excluded: chain a residue 387 VAL 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 c residue 1 MET Chi-restraints excluded: chain c residue 46 ASP Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain f residue 44 MET Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 206 LYS Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 206 LYS 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: 7.9990 chunk 429 optimal weight: 50.0000 chunk 296 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 272 optimal weight: 40.0000 chunk 383 optimal weight: 0.0980 chunk 573 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 543 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- 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 21 ASN ** B 156 ASN ** 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 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN I 348 ASN J 25 HIS ** J 27 GLN ** 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 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN b 72 GLN ** b 156 ASN ** 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** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 186 GLN ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 53708 Z= 0.173 Angle : 0.539 14.267 73867 Z= 0.276 Chirality : 0.038 0.190 8324 Planarity : 0.004 0.059 9006 Dihedral : 17.334 176.894 9470 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.06 % Allowed : 17.81 % Favored : 80.13 % 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: 0.06 (0.11), residues: 6192 helix: 1.50 (0.12), residues: 2004 sheet: 0.86 (0.17), residues: 1000 loop : -1.25 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 215 HIS 0.012 0.001 HIS d 159 PHE 0.017 0.001 PHE K 195 TYR 0.045 0.002 TYR f 157 ARG 0.006 0.000 ARG d 155 *********************** 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 212 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 112 time to evaluate : 5.700 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: F 250 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4898 (tt) REVERT: K 1 MET cc_start: 0.8422 (tmm) cc_final: 0.7906 (tmm) outliers start: 100 outliers final: 40 residues processed: 202 average time/residue: 0.5978 time to fit residues: 212.2532 Evaluate side-chains 148 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP 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 140 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 351 ARG Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain a residue 9 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 140 THR Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 140 THR 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 98 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 206 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 8.9990 chunk 344 optimal weight: 0.2980 chunk 8 optimal weight: 50.0000 chunk 451 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 518 optimal weight: 1.9990 chunk 419 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 chunk 309 optimal weight: 30.0000 chunk 544 optimal weight: 3.9990 chunk 153 optimal weight: 0.0070 overall best weight: 2.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** 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 242 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 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 156 ASN ** 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** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 160 ASN ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5118 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 53708 Z= 0.143 Angle : 0.525 12.369 73867 Z= 0.265 Chirality : 0.038 0.314 8324 Planarity : 0.003 0.059 9006 Dihedral : 17.233 177.414 9470 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.44 % Allowed : 18.76 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 6192 helix: 1.66 (0.12), residues: 1996 sheet: 0.94 (0.17), residues: 988 loop : -1.22 (0.11), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 193 HIS 0.005 0.001 HIS K 68 PHE 0.015 0.001 PHE b 40 TYR 0.046 0.001 TYR f 157 ARG 0.009 0.000 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 184 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 114 time to evaluate : 5.904 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: F 250 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4868 (tt) REVERT: K 1 MET cc_start: 0.8252 (tmm) cc_final: 0.7955 (tmm) REVERT: K 62 PHE cc_start: 0.8200 (t80) cc_final: 0.7971 (t80) REVERT: K 206 ASN cc_start: 0.6549 (t0) cc_final: 0.5681 (p0) outliers start: 70 outliers final: 47 residues processed: 179 average time/residue: 0.6088 time to fit residues: 190.4007 Evaluate side-chains 149 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 101 time to evaluate : 5.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 E residue 181 ILE Chi-restraints excluded: chain F residue 80 ASP 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 71 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 197 LYS Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 420 LYS 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 c residue 167 THR Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 140 THR 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 100 VAL Chi-restraints excluded: chain h residue 206 LYS 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 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 5.9990 chunk 546 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 356 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 607 optimal weight: 10.0000 chunk 504 optimal weight: 40.0000 chunk 281 optimal weight: 50.0000 chunk 50 optimal weight: 40.0000 chunk 200 optimal weight: 30.0000 chunk 318 optimal weight: 3.9990 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 81 ASN ** A 132 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 156 ASN ** 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** E 186 GLN E 260 GLN E 348 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 289 HIS ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN ** 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** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 53708 Z= 0.205 Angle : 0.569 16.326 73867 Z= 0.290 Chirality : 0.038 0.392 8324 Planarity : 0.004 0.082 9006 Dihedral : 17.233 178.371 9470 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 1.92 % Allowed : 18.88 % Favored : 79.20 % 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: 0.24 (0.11), residues: 6192 helix: 1.68 (0.12), residues: 2000 sheet: 0.84 (0.16), residues: 996 loop : -1.10 (0.11), residues: 3196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 347 HIS 0.010 0.001 HIS A 203 PHE 0.040 0.001 PHE a 232 TYR 0.046 0.002 TYR f 157 ARG 0.013 0.001 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 196 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 103 time to evaluate : 5.952 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: J 105 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7191 (p0) REVERT: K 206 ASN cc_start: 0.6618 (t0) cc_final: 0.5894 (p0) outliers start: 93 outliers final: 62 residues processed: 186 average time/residue: 0.6387 time to fit residues: 206.4170 Evaluate side-chains 160 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 97 time to evaluate : 5.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 114 PHE 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 72 ILE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 281 MET 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 c residue 1 MET Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 140 THR 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 f residue 270 ASP Chi-restraints excluded: chain f residue 327 LEU Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 206 LYS 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 72 ILE 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: 40.0000 chunk 346 optimal weight: 2.9990 chunk 443 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 511 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 605 optimal weight: 50.0000 chunk 378 optimal weight: 40.0000 chunk 369 optimal weight: 50.0000 chunk 279 optimal weight: 9.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- 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 89 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 310 GLN ** I 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 253 GLN ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 ASN ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 227 HIS ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 260 GLN f 91 GLN f 96 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 348 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 53708 Z= 0.278 Angle : 0.650 13.761 73867 Z= 0.336 Chirality : 0.039 0.301 8324 Planarity : 0.005 0.085 9006 Dihedral : 17.352 179.736 9470 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 27.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.21 % Allowed : 19.00 % Favored : 78.79 % 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: 0.05 (0.11), residues: 6192 helix: 1.42 (0.11), residues: 1980 sheet: 0.71 (0.17), residues: 948 loop : -1.09 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 347 HIS 0.008 0.001 HIS K 169 PHE 0.015 0.002 PHE b 40 TYR 0.028 0.002 TYR K 198 ARG 0.010 0.001 ARG D 169 *********************** 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 194 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 87 time to evaluate : 5.143 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: C 46 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4922 (p0) REVERT: J 105 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7275 (p0) REVERT: a 119 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8337 (pttm) outliers start: 107 outliers final: 74 residues processed: 184 average time/residue: 0.6428 time to fit residues: 204.3371 Evaluate side-chains 162 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 85 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 F residue 80 ASP Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 351 ARG 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 72 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 70 LEU Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 281 MET 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 c residue 46 ASP Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain d residue 35 ARG Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 140 THR 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 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 106 ASP Chi-restraints excluded: chain h residue 206 LYS 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 38 ASP Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE 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: 30.0000 chunk 241 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 118 optimal weight: 50.0000 chunk 117 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 412 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 56 optimal weight: 50.0000 chunk 475 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 156 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** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 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** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 186 GLN g 242 GLN h 348 ASN ** i 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 53708 Z= 0.238 Angle : 0.597 14.408 73867 Z= 0.306 Chirality : 0.038 0.408 8324 Planarity : 0.004 0.065 9006 Dihedral : 17.351 179.687 9470 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.74 % Favored : 94.25 % Rotamer: Outliers : 1.83 % Allowed : 19.64 % Favored : 78.52 % 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: 0.14 (0.11), residues: 6192 helix: 1.49 (0.12), residues: 1996 sheet: 0.72 (0.16), residues: 992 loop : -1.06 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 362 HIS 0.014 0.001 HIS A 203 PHE 0.016 0.001 PHE f 323 TYR 0.021 0.002 TYR J 128 ARG 0.008 0.001 ARG f 156 *********************** 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 175 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 86 time to evaluate : 5.351 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: A 281 MET cc_start: 0.4268 (tpt) cc_final: 0.3973 (tpt) REVERT: J 105 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7349 (p0) REVERT: K 206 ASN cc_start: 0.6716 (t0) cc_final: 0.6393 (p0) outliers start: 89 outliers final: 64 residues processed: 166 average time/residue: 0.6294 time to fit residues: 179.6662 Evaluate side-chains 150 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 85 time to evaluate : 5.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 211 ASP 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 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 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 244 VAL Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 207 ARG Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain a residue 9 THR Chi-restraints excluded: chain a residue 281 MET 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 c residue 46 ASP Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain d residue 35 ARG Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 250 LEU Chi-restraints excluded: chain d residue 334 ASP 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 f residue 270 ASP Chi-restraints excluded: chain g residue 68 VAL Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 206 LYS Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 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: 0.0770 chunk 579 optimal weight: 7.9990 chunk 529 optimal weight: 20.0000 chunk 564 optimal weight: 3.9990 chunk 339 optimal weight: 8.9990 chunk 245 optimal weight: 30.0000 chunk 442 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 509 optimal weight: 9.9990 chunk 533 optimal weight: 4.9990 chunk 562 optimal weight: 40.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- 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 156 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** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 242 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 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** ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 53708 Z= 0.174 Angle : 0.560 12.406 73867 Z= 0.283 Chirality : 0.038 0.336 8324 Planarity : 0.004 0.068 9006 Dihedral : 17.278 179.685 9470 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.30 % Allowed : 20.34 % Favored : 78.36 % 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: 1.68 (0.12), residues: 1994 sheet: 0.73 (0.17), residues: 964 loop : -1.05 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 362 HIS 0.005 0.001 HIS K 68 PHE 0.014 0.001 PHE f 323 TYR 0.022 0.001 TYR J 128 ARG 0.006 0.000 ARG K 196 *********************** 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 157 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 94 time to evaluate : 5.506 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: J 105 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7353 (p0) REVERT: K 9 PHE cc_start: 0.7788 (m-80) cc_final: 0.7540 (m-80) outliers start: 63 outliers final: 57 residues processed: 152 average time/residue: 0.6254 time to fit residues: 164.4325 Evaluate side-chains 145 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 87 time to evaluate : 5.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP 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 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 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 244 VAL 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 105 ASP Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP 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 422 LEU Chi-restraints excluded: chain b residue 24 SER Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 249 VAL Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 334 ASP Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR 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 302 GLU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 206 LYS Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE 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: 9.9990 chunk 596 optimal weight: 9.9990 chunk 364 optimal weight: 30.0000 chunk 282 optimal weight: 0.9990 chunk 414 optimal weight: 20.0000 chunk 625 optimal weight: 50.0000 chunk 575 optimal weight: 30.0000 chunk 498 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 384 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 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** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 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** ** 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 moved from start: 0.5644 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= 0.204 Angle : 0.576 12.642 73867 Z= 0.292 Chirality : 0.037 0.341 8324 Planarity : 0.004 0.067 9006 Dihedral : 17.249 179.490 9470 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.04 % Rotamer: Outliers : 1.26 % Allowed : 20.55 % Favored : 78.19 % 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: 0.24 (0.11), residues: 6192 helix: 1.67 (0.12), residues: 1996 sheet: 0.79 (0.17), residues: 946 loop : -1.04 (0.11), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 362 HIS 0.005 0.001 HIS J 19 PHE 0.022 0.001 PHE K 195 TYR 0.052 0.002 TYR F 157 ARG 0.018 0.001 ARG J 207 ********************** 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 153 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 92 time to evaluate : 5.545 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: J 105 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7323 (p0) outliers start: 61 outliers final: 56 residues processed: 149 average time/residue: 0.6446 time to fit residues: 165.7360 Evaluate side-chains 144 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 87 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 211 ASP 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 140 THR Chi-restraints excluded: chain D residue 172 VAL 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 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 244 VAL Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain K residue 37 MET Chi-restraints excluded: chain K residue 46 TYR Chi-restraints excluded: chain K residue 81 ASP 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 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 46 ASP Chi-restraints excluded: chain c residue 76 LEU Chi-restraints excluded: chain c residue 83 LEU Chi-restraints excluded: chain c residue 167 THR Chi-restraints excluded: chain d residue 35 ARG Chi-restraints excluded: chain d residue 140 THR Chi-restraints excluded: chain d residue 334 ASP 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 302 GLU Chi-restraints excluded: chain g residue 307 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain h residue 106 ASP Chi-restraints excluded: chain h residue 206 LYS Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 274 ILE Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 72 ILE 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: 1.9990 chunk 530 optimal weight: 6.9990 chunk 152 optimal weight: 0.0070 chunk 459 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 498 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 512 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 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** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN ** a 81 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.036556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.024195 restraints weight = 896103.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.024505 restraints weight = 611992.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.024647 restraints weight = 472321.155| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 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 = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 53708 Z= 0.154 Angle : 0.547 12.122 73867 Z= 0.275 Chirality : 0.038 0.314 8324 Planarity : 0.004 0.068 9006 Dihedral : 17.207 179.603 9470 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.22 % Allowed : 20.57 % Favored : 78.22 % 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: 0.29 (0.11), residues: 6192 helix: 1.76 (0.12), residues: 1994 sheet: 0.81 (0.17), residues: 946 loop : -1.04 (0.11), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 362 HIS 0.006 0.001 HIS K 68 PHE 0.016 0.001 PHE f 323 TYR 0.046 0.001 TYR F 157 ARG 0.011 0.000 ARG h 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.05 seconds wall clock time: 146 minutes 56.22 seconds (8816.22 seconds total)