Starting phenix.real_space_refine on Sun Feb 25 10:09:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3k_25661/02_2024/7t3k_25661.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.055 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 120 5.49 5 S 58 5.16 5 C 31428 2.51 5 N 9208 2.21 5 O 9806 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 PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50620 Number of models: 1 Model: "" Number of chains: 22 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 Time building chain proxies: 26.96, per 1000 atoms: 0.53 Number of scatterers: 50620 At special positions: 0 Unit cell: (157.5, 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 120 15.00 O 9806 8.00 N 9208 7.00 C 31428 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: 19.37 Conformation dependent library (CDL) restraints added in 9.0 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 10 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 16.05 Creating SS restraints... 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: 3.506A 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: 3.774A 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: 3.686A pdb=" N LEU A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.728A 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: 3.902A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.597A 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: 3.582A 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: 3.837A 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: 3.522A pdb=" N PHE J 55 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 5.280A 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: 3.754A 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: 3.872A 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 removed outlier: 3.567A pdb=" N PHE K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 198 " --> pdb=" O ASN K 194 " (cutoff:3.500A) 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: 3.505A 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: 3.774A 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: 3.686A pdb=" N LEU a 406 " --> pdb=" O ASP a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 409 through 431 removed outlier: 3.728A 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: 3.898A pdb=" N GLY b 312 " --> pdb=" O PRO b 309 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 36 removed outlier: 3.992A 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: 3.582A 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: 3.837A 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: 3.512A 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 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: 3.576A 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: 6.730A 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: 7.392A 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: 4.207A 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: 7.392A 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=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: 6.717A 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: 3.575A 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: 3.806A 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: 3.829A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 179 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.648A 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: 4.628A 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: 4.513A 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: 4.558A 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: 6.846A 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: 4.588A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.231A 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: 6.549A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.425A 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: 6.472A 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: 7.119A pdb=" N VAL H 177 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 4.571A 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: 3.823A 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: 3.823A 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: 6.439A 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=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: 4.263A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 7.229A 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: 6.967A 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: 6.313A 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: 6.942A 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: 3.524A 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: 3.603A 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: 3.505A 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: 4.220A 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: 5.782A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.915A 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: 5.782A pdb=" N HIS K 19 " --> pdb=" O LEU i 95 " (cutoff:3.500A) removed outlier: 7.915A 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: 5.658A 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: 5.908A 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: 6.730A 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: 8.144A 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: 7.421A 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: 8.144A 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: 7.421A 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: 4.695A 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: 3.880A 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=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: 3.828A 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: 6.923A 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: 6.604A 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=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: 4.557A 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: 4.543A 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: 4.650A 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: 4.589A 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: 6.549A 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: 4.270A 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: 4.550A 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: 6.440A 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: 4.556A 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: 6.483A 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: 3.524A 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 2099 hydrogen bonds defined for protein. 5748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 22.39 Time building geometry restraints manager: 21.03 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: 10062 1.33 - 1.45: 12948 1.45 - 1.57: 28578 1.57 - 1.69: 242 1.69 - 1.81: 90 Bond restraints: 51920 Sorted by residual: bond pdb=" C ARG K 116 " pdb=" O ARG K 116 " ideal model delta sigma weight residual 1.244 1.205 0.039 9.40e-03 1.13e+04 1.68e+01 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 3.45e+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 3.39e+00 bond pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 1.525 1.502 0.023 1.29e-02 6.01e+03 3.20e+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 3.16e+00 ... (remaining 51915 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.25: 169 102.25 - 110.49: 14645 110.49 - 118.74: 27673 118.74 - 126.98: 27653 126.98 - 135.23: 982 Bond angle restraints: 71122 Sorted by residual: angle pdb=" N SER K 92 " pdb=" CA SER K 92 " pdb=" C SER K 92 " ideal model delta sigma weight residual 112.04 105.15 6.89 1.44e+00 4.82e-01 2.29e+01 angle pdb=" N PRO K 34 " pdb=" CA PRO K 34 " pdb=" C PRO K 34 " ideal model delta sigma weight residual 114.68 109.78 4.90 1.04e+00 9.25e-01 2.22e+01 angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C LYS g 77 " pdb=" N THR g 78 " pdb=" CA THR g 78 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C ARG K 116 " pdb=" N PRO K 117 " pdb=" CA PRO K 117 " ideal model delta sigma weight residual 119.84 114.57 5.27 1.25e+00 6.40e-01 1.78e+01 ... (remaining 71117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 30230 35.78 - 71.56: 986 71.56 - 107.33: 78 107.33 - 143.11: 2 143.11 - 178.89: 12 Dihedral angle restraints: 31308 sinusoidal: 13332 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 52.41 147.59 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 52.46 147.54 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 52.68 147.32 1 1.50e+01 4.44e-03 7.86e+01 ... (remaining 31305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6933 0.066 - 0.132: 995 0.132 - 0.197: 65 0.197 - 0.263: 14 0.263 - 0.329: 5 Chirality restraints: 8012 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 2.71e+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 2.67e+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 2.30e+00 ... (remaining 8009 not shown) Planarity restraints: 8928 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 8.12e-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 8925 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 6736 2.76 - 3.29: 46993 3.29 - 3.83: 91755 3.83 - 4.36: 109541 4.36 - 4.90: 181211 Nonbonded interactions: 436236 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 2.244 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 2.282 2.440 ... (remaining 436231 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' } 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: 1.440 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: 0.030 Extract box with map and model: 7.430 Check model and map are aligned: 0.730 Set scattering table: 0.420 Process input model: 142.170 Find NCS groups from input model: 5.020 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 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 51920 Z= 0.238 Angle : 0.745 12.205 71122 Z= 0.403 Chirality : 0.046 0.329 8012 Planarity : 0.007 0.127 8928 Dihedral : 17.272 178.888 19700 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.01 % Rotamer: Outliers : 0.52 % Allowed : 17.27 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 6192 helix: -1.29 (0.09), residues: 1960 sheet: 0.41 (0.17), residues: 966 loop : -1.83 (0.10), residues: 3266 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 0.000 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 1170 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1145 time to evaluate : 5.710 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 ASP cc_start: 0.5465 (m-30) cc_final: 0.5218 (p0) REVERT: D 232 VAL cc_start: 0.7766 (t) cc_final: 0.7514 (t) REVERT: D 344 TYR cc_start: 0.4969 (t80) cc_final: 0.4309 (t80) REVERT: E 74 ASN cc_start: 0.7409 (p0) cc_final: 0.7010 (p0) REVERT: H 262 SER cc_start: 0.8701 (p) cc_final: 0.8283 (t) REVERT: K 46 TYR cc_start: 0.8127 (m-10) cc_final: 0.6246 (m-80) REVERT: a 303 THR cc_start: 0.8615 (m) cc_final: 0.8096 (m) REVERT: d 284 ARG cc_start: 0.3652 (mtp180) cc_final: 0.3208 (mmt180) outliers start: 25 outliers final: 5 residues processed: 1162 average time/residue: 0.7001 time to fit residues: 1314.4692 Evaluate side-chains 574 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 569 time to evaluate : 5.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain a residue 324 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 9.9990 chunk 472 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 489 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 297 optimal weight: 2.9990 chunk 364 optimal weight: 9.9990 chunk 566 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 186 GLN D 227 HIS ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN E 148 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 HIS J 194 ASN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 188 HIS a 203 HIS ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 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** c 29 HIS d 159 HIS d 281 ASN ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 342 GLN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 160 ASN f 182 ASN f 310 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 ASN ** h 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 51920 Z= 0.262 Angle : 0.650 13.823 71122 Z= 0.332 Chirality : 0.042 0.263 8012 Planarity : 0.005 0.073 8928 Dihedral : 14.619 178.473 8720 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.24 % Allowed : 19.64 % Favored : 77.12 % 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: -0.82 (0.10), residues: 6192 helix: 0.29 (0.11), residues: 1952 sheet: 0.96 (0.17), residues: 912 loop : -1.54 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP e 330 HIS 0.008 0.001 HIS i 227 PHE 0.036 0.002 PHE C 25 TYR 0.024 0.002 TYR G 324 ARG 0.013 0.001 ARG E 191 *********************** 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 759 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 602 time to evaluate : 5.602 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: A 145 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7035 (pp) REVERT: A 290 ASP cc_start: 0.7308 (t70) cc_final: 0.6892 (t0) REVERT: B 166 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (t0) REVERT: C 25 PHE cc_start: 0.7345 (t80) cc_final: 0.6982 (t80) REVERT: D 232 VAL cc_start: 0.7624 (t) cc_final: 0.7399 (t) REVERT: E 74 ASN cc_start: 0.7306 (p0) cc_final: 0.7069 (p0) REVERT: H 262 SER cc_start: 0.8518 (p) cc_final: 0.8171 (t) REVERT: I 181 ILE cc_start: 0.8720 (mp) cc_final: 0.8487 (mt) REVERT: K 46 TYR cc_start: 0.8106 (m-80) cc_final: 0.7893 (m-80) REVERT: K 147 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (mm) REVERT: K 220 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7346 (t0) REVERT: a 290 ASP cc_start: 0.7200 (p0) cc_final: 0.6804 (p0) REVERT: a 297 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8344 (p) REVERT: d 284 ARG cc_start: 0.4260 (mtp180) cc_final: 0.3616 (mmt180) REVERT: h 257 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (pttp) outliers start: 157 outliers final: 70 residues processed: 702 average time/residue: 0.6017 time to fit residues: 710.0446 Evaluate side-chains 540 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 464 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 220 ASP Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 286 VAL Chi-restraints excluded: chain a residue 297 VAL Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 291 SER Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 126 SER Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 274 ILE Chi-restraints excluded: chain e residue 114 PHE Chi-restraints excluded: chain e residue 137 LEU Chi-restraints excluded: chain e residue 277 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 339 VAL Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 37 LEU Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 471 optimal weight: 20.0000 chunk 385 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 567 optimal weight: 10.0000 chunk 613 optimal weight: 4.9990 chunk 505 optimal weight: 3.9990 chunk 562 optimal weight: 30.0000 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN E 348 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN I 348 ASN J 25 HIS J 154 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 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** b 306 HIS ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 348 ASN ** f 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 281 ASN f 310 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 96 GLN h 183 HIS h 310 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 51920 Z= 0.342 Angle : 0.671 12.566 71122 Z= 0.345 Chirality : 0.042 0.305 8012 Planarity : 0.005 0.070 8928 Dihedral : 14.571 178.451 8713 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.00 % Allowed : 20.14 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 6192 helix: 0.72 (0.11), residues: 1982 sheet: 0.97 (0.17), residues: 918 loop : -1.39 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 330 HIS 0.012 0.001 HIS f 343 PHE 0.034 0.002 PHE b 31 TYR 0.023 0.002 TYR A 336 ARG 0.012 0.001 ARG e 75 *********************** 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 699 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 505 time to evaluate : 5.255 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: A 145 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6858 (pp) REVERT: B 166 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8367 (t0) REVERT: D 119 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5521 (mt) REVERT: D 184 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6713 (mp) REVERT: E 92 SER cc_start: 0.8603 (m) cc_final: 0.8399 (t) REVERT: b 209 THR cc_start: 0.7489 (m) cc_final: 0.7179 (m) REVERT: d 161 LEU cc_start: 0.6520 (pp) cc_final: 0.6125 (pp) REVERT: d 202 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3966 (mt) REVERT: d 284 ARG cc_start: 0.4271 (mtp180) cc_final: 0.3988 (mmt180) REVERT: e 287 ASP cc_start: 0.5671 (t0) cc_final: 0.5420 (t0) REVERT: h 150 PHE cc_start: 0.6519 (m-10) cc_final: 0.6240 (m-10) REVERT: h 257 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7763 (pttp) REVERT: h 354 VAL cc_start: 0.6504 (OUTLIER) cc_final: 0.6298 (t) REVERT: i 80 ASP cc_start: 0.6414 (OUTLIER) cc_final: 0.6016 (m-30) outliers start: 194 outliers final: 101 residues processed: 644 average time/residue: 0.6451 time to fit residues: 708.5650 Evaluate side-chains 515 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 406 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 247 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 294 ASP Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 194 ASN Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 103 ARG Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 265 LEU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 286 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 306 HIS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 126 SER Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 332 LEU Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 294 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 75 ARG Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 285 THR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 161 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 257 LYS Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 80 ASP Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 10.0000 chunk 426 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 270 optimal weight: 0.3980 chunk 381 optimal weight: 5.9990 chunk 569 optimal weight: 9.9990 chunk 603 optimal weight: 40.0000 chunk 297 optimal weight: 3.9990 chunk 539 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 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** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 248 GLN ** f 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 ASN g 248 GLN ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 51920 Z= 0.293 Angle : 0.628 15.208 71122 Z= 0.321 Chirality : 0.041 0.234 8012 Planarity : 0.005 0.062 8928 Dihedral : 14.547 178.366 8709 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.57 % Allowed : 21.15 % Favored : 75.29 % 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: -0.31 (0.11), residues: 6192 helix: 1.04 (0.11), residues: 1968 sheet: 0.85 (0.17), residues: 954 loop : -1.37 (0.11), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 330 HIS 0.028 0.001 HIS b 306 PHE 0.032 0.002 PHE C 44 TYR 0.032 0.002 TYR d 266 ARG 0.007 0.001 ARG f 117 *********************** 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 640 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 467 time to evaluate : 5.090 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: A 145 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6833 (pp) REVERT: A 429 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (tp) REVERT: B 166 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8449 (t0) REVERT: D 119 LEU cc_start: 0.5838 (OUTLIER) cc_final: 0.5548 (mt) REVERT: F 64 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: K 11 ILE cc_start: 0.9531 (mt) cc_final: 0.9146 (tt) REVERT: a 290 ASP cc_start: 0.7211 (p0) cc_final: 0.6874 (p0) REVERT: b 209 THR cc_start: 0.7567 (m) cc_final: 0.7193 (m) REVERT: d 161 LEU cc_start: 0.6810 (pp) cc_final: 0.6543 (pp) REVERT: d 284 ARG cc_start: 0.4712 (mtp180) cc_final: 0.4285 (mmt180) REVERT: i 80 ASP cc_start: 0.6356 (OUTLIER) cc_final: 0.5988 (m-30) outliers start: 173 outliers final: 103 residues processed: 595 average time/residue: 0.5644 time to fit residues: 570.5763 Evaluate side-chains 512 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 403 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain H residue 354 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 194 ASN Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 286 VAL Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 219 ILE Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 294 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 217 LEU Chi-restraints excluded: chain f residue 285 THR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 230 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain h residue 354 VAL Chi-restraints excluded: chain h residue 355 PHE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 80 ASP Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 0.0030 chunk 342 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 449 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 514 optimal weight: 9.9990 chunk 416 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 307 optimal weight: 8.9990 chunk 541 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 262 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** b 306 HIS d 129 ASN ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 51920 Z= 0.241 Angle : 0.601 12.423 71122 Z= 0.305 Chirality : 0.041 0.363 8012 Planarity : 0.004 0.062 8928 Dihedral : 14.526 178.340 8709 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.69 % Allowed : 21.58 % Favored : 74.73 % 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: -0.19 (0.11), residues: 6192 helix: 1.23 (0.12), residues: 1968 sheet: 0.81 (0.17), residues: 932 loop : -1.31 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP d 168 HIS 0.012 0.001 HIS f 275 PHE 0.047 0.002 PHE C 44 TYR 0.024 0.002 TYR i 157 ARG 0.005 0.000 ARG D 156 *********************** 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 659 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 480 time to evaluate : 5.042 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: A 20 PHE cc_start: 0.7816 (t80) cc_final: 0.7382 (t80) REVERT: A 145 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6705 (pp) REVERT: A 429 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8804 (tp) REVERT: B 166 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (t0) REVERT: D 119 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5562 (mt) REVERT: E 349 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7416 (mp) REVERT: F 64 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7268 (ttp80) REVERT: J 198 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: K 98 LEU cc_start: 0.8786 (mp) cc_final: 0.8535 (mp) REVERT: a 242 LYS cc_start: 0.6409 (tptp) cc_final: 0.6191 (mmmm) REVERT: a 290 ASP cc_start: 0.7462 (p0) cc_final: 0.7063 (p0) REVERT: b 209 THR cc_start: 0.7600 (m) cc_final: 0.7211 (m) REVERT: c 81 ASP cc_start: 0.4638 (t0) cc_final: 0.3414 (t0) REVERT: c 117 MET cc_start: 0.0999 (mpp) cc_final: 0.0323 (mtm) REVERT: d 161 LEU cc_start: 0.6873 (pp) cc_final: 0.6644 (pp) REVERT: d 284 ARG cc_start: 0.4885 (mtp180) cc_final: 0.4595 (mmt180) REVERT: i 80 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.5843 (m-30) outliers start: 179 outliers final: 108 residues processed: 607 average time/residue: 0.6300 time to fit residues: 659.8725 Evaluate side-chains 533 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 417 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 194 ASN Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 77 ARG Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain b residue 306 HIS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 70 LEU Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 294 ASP Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 31 LEU Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 217 LEU Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 80 ASP Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 9.9990 chunk 543 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 354 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 603 optimal weight: 30.0000 chunk 501 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 GLN ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 GLN ** b 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 306 HIS ** d 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 260 GLN ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 51920 Z= 0.317 Angle : 0.644 15.520 71122 Z= 0.326 Chirality : 0.042 0.340 8012 Planarity : 0.004 0.061 8928 Dihedral : 14.533 179.339 8709 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.42 % Allowed : 22.49 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 6192 helix: 1.22 (0.12), residues: 1974 sheet: 0.77 (0.17), residues: 944 loop : -1.32 (0.11), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP d 168 HIS 0.020 0.001 HIS b 306 PHE 0.041 0.002 PHE C 44 TYR 0.027 0.002 TYR e 324 ARG 0.008 0.001 ARG b 315 *********************** 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 582 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 416 time to evaluate : 5.743 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: A 145 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6691 (pp) REVERT: B 166 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8628 (t0) REVERT: C 40 ILE cc_start: 0.1010 (OUTLIER) cc_final: 0.0493 (mm) REVERT: D 119 LEU cc_start: 0.5899 (OUTLIER) cc_final: 0.5659 (mt) REVERT: F 64 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7405 (ttp80) REVERT: J 198 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: K 27 GLN cc_start: 0.8693 (mm110) cc_final: 0.8336 (tp-100) REVERT: a 157 GLN cc_start: 0.7656 (pp30) cc_final: 0.7376 (pp30) REVERT: d 284 ARG cc_start: 0.5049 (mtp180) cc_final: 0.4467 (mmt180) REVERT: e 332 LEU cc_start: 0.7015 (mt) cc_final: 0.6795 (mp) REVERT: f 44 MET cc_start: 0.5550 (mtp) cc_final: 0.4944 (mtm) REVERT: g 258 LYS cc_start: 0.7262 (mmmt) cc_final: 0.6996 (mmmt) outliers start: 166 outliers final: 116 residues processed: 535 average time/residue: 0.5825 time to fit residues: 533.2233 Evaluate side-chains 509 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 387 time to evaluate : 5.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain F residue 64 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 182 ASN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain H residue 350 ILE Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 350 ILE Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 198 TYR Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 194 ASN Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 116 ASP Chi-restraints excluded: chain a residue 196 THR Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain e residue 294 ASP Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 116 LEU Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 217 LEU Chi-restraints excluded: chain f residue 285 THR Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 343 optimal weight: 0.0050 chunk 440 optimal weight: 5.9990 chunk 341 optimal weight: 0.9980 chunk 508 optimal weight: 0.9980 chunk 337 optimal weight: 7.9990 chunk 601 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 396 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** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 51920 Z= 0.186 Angle : 0.599 13.564 71122 Z= 0.300 Chirality : 0.040 0.295 8012 Planarity : 0.004 0.060 8928 Dihedral : 14.527 179.979 8709 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.02 % Favored : 94.96 % Rotamer: Outliers : 2.80 % Allowed : 23.66 % Favored : 73.54 % 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: 1.40 (0.12), residues: 1958 sheet: 0.80 (0.17), residues: 944 loop : -1.25 (0.11), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP d 168 HIS 0.010 0.001 HIS f 275 PHE 0.030 0.002 PHE g 195 TYR 0.032 0.002 TYR b 314 ARG 0.008 0.000 ARG I 269 *********************** 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 580 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 444 time to evaluate : 5.717 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: B 166 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8489 (t70) REVERT: C 40 ILE cc_start: 0.0626 (OUTLIER) cc_final: -0.0056 (mm) REVERT: D 119 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5713 (mt) REVERT: E 91 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7212 (mm-40) REVERT: E 349 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7410 (mp) REVERT: K 40 LYS cc_start: 0.8883 (mttt) cc_final: 0.8629 (ptpt) REVERT: c 117 MET cc_start: 0.1333 (mpp) cc_final: 0.0660 (mtm) REVERT: d 44 MET cc_start: 0.2859 (mpp) cc_final: 0.2615 (mpp) REVERT: d 284 ARG cc_start: 0.5073 (mtp180) cc_final: 0.4342 (mmt180) REVERT: f 44 MET cc_start: 0.5641 (mtp) cc_final: 0.5015 (mtm) outliers start: 136 outliers final: 93 residues processed: 543 average time/residue: 0.5882 time to fit residues: 543.5281 Evaluate side-chains 489 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 392 time to evaluate : 5.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain b residue 290 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 74 ASN Chi-restraints excluded: chain e residue 117 ARG Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 247 SER Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 208 ASP Chi-restraints excluded: chain i residue 327 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 chunk 181 optimal weight: 0.2980 chunk 118 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 382 optimal weight: 20.0000 chunk 409 optimal weight: 0.1980 chunk 297 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 393 ASN ** A 396 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** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 51920 Z= 0.190 Angle : 0.609 13.791 71122 Z= 0.303 Chirality : 0.041 0.299 8012 Planarity : 0.004 0.060 8928 Dihedral : 14.479 178.512 8708 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.35 % Favored : 94.64 % Rotamer: Outliers : 2.54 % Allowed : 23.99 % Favored : 73.47 % 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: -0.02 (0.11), residues: 6192 helix: 1.45 (0.12), residues: 1956 sheet: 0.82 (0.17), residues: 944 loop : -1.23 (0.11), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP b 289 HIS 0.008 0.001 HIS f 275 PHE 0.064 0.002 PHE e 195 TYR 0.045 0.002 TYR b 314 ARG 0.007 0.000 ARG i 134 *********************** 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 547 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 424 time to evaluate : 6.270 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: C 40 ILE cc_start: 0.0381 (OUTLIER) cc_final: -0.0191 (mm) REVERT: D 212 ASP cc_start: 0.7198 (p0) cc_final: 0.6667 (m-30) REVERT: E 91 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7253 (mm-40) REVERT: E 349 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7411 (mp) REVERT: K 27 GLN cc_start: 0.8705 (mm110) cc_final: 0.8349 (tp-100) REVERT: a 157 GLN cc_start: 0.7422 (pp30) cc_final: 0.7192 (pp30) REVERT: a 281 MET cc_start: 0.1346 (tpt) cc_final: 0.0603 (mmm) REVERT: b 247 TRP cc_start: 0.4888 (OUTLIER) cc_final: 0.3981 (m-90) REVERT: b 286 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5841 (mm) REVERT: c 117 MET cc_start: 0.1503 (mpp) cc_final: 0.1099 (mtm) REVERT: d 44 MET cc_start: 0.3064 (mpp) cc_final: 0.2787 (mpp) REVERT: d 284 ARG cc_start: 0.5131 (mtp180) cc_final: 0.4256 (mmt180) REVERT: f 44 MET cc_start: 0.5588 (mtp) cc_final: 0.4970 (mtm) outliers start: 123 outliers final: 92 residues processed: 511 average time/residue: 0.6138 time to fit residues: 536.1887 Evaluate side-chains 494 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 398 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 77 LYS Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ASN Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 195 PHE Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 247 TRP Chi-restraints excluded: chain b residue 286 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 46 ASP Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 198 LEU Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain f residue 308 THR Chi-restraints excluded: chain g residue 34 GLU Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 247 SER Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 80 ASP Chi-restraints excluded: chain i residue 137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 6.9990 chunk 576 optimal weight: 8.9990 chunk 525 optimal weight: 3.9990 chunk 560 optimal weight: 9.9990 chunk 337 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 440 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 506 optimal weight: 10.0000 chunk 530 optimal weight: 7.9990 chunk 558 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 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** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 GLN J 26 HIS J 216 HIS ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 89 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** d 183 HIS ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 51920 Z= 0.307 Angle : 0.663 13.962 71122 Z= 0.333 Chirality : 0.042 0.277 8012 Planarity : 0.005 0.064 8928 Dihedral : 14.506 178.069 8708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.70 % Allowed : 24.18 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6192 helix: 1.38 (0.12), residues: 1952 sheet: 0.63 (0.17), residues: 996 loop : -1.24 (0.11), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 394 HIS 0.010 0.001 HIS b 306 PHE 0.031 0.002 PHE d 114 TYR 0.029 0.002 TYR b 314 ARG 0.008 0.001 ARG f 156 *********************** 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 526 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 395 time to evaluate : 5.617 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 40 ILE cc_start: 0.0083 (OUTLIER) cc_final: -0.0516 (mm) REVERT: D 214 LEU cc_start: 0.7210 (tt) cc_final: 0.6990 (tt) REVERT: E 349 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7465 (mp) REVERT: K 27 GLN cc_start: 0.8805 (mm110) cc_final: 0.8452 (tp-100) REVERT: a 157 GLN cc_start: 0.7494 (pp30) cc_final: 0.7239 (pp30) REVERT: d 44 MET cc_start: 0.3056 (mpp) cc_final: 0.2769 (mpp) REVERT: d 284 ARG cc_start: 0.5337 (mtp180) cc_final: 0.4103 (mmt180) outliers start: 131 outliers final: 99 residues processed: 492 average time/residue: 0.5974 time to fit residues: 502.4566 Evaluate side-chains 479 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 378 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 240 ASP Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 2 ASN Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 362 TRP Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 283 LEU Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 46 ASP Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain g residue 34 GLU Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 247 SER Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 80 ASP Chi-restraints excluded: chain i residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 50.0000 chunk 592 optimal weight: 9.9990 chunk 361 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 411 optimal weight: 50.0000 chunk 621 optimal weight: 20.0000 chunk 572 optimal weight: 30.0000 chunk 495 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 382 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 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** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 51920 Z= 0.317 Angle : 0.669 14.590 71122 Z= 0.334 Chirality : 0.042 0.292 8012 Planarity : 0.004 0.061 8928 Dihedral : 14.538 178.170 8708 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.41 % Allowed : 24.73 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 6192 helix: 1.31 (0.12), residues: 1954 sheet: 0.65 (0.17), residues: 956 loop : -1.25 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 394 HIS 0.008 0.001 HIS b 306 PHE 0.035 0.002 PHE b 40 TYR 0.023 0.002 TYR J 46 ARG 0.015 0.001 ARG C 68 ********************** 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 504 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 387 time to evaluate : 5.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 MET cc_start: 0.6349 (mmp) cc_final: 0.6066 (mmp) REVERT: B 166 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8639 (t70) REVERT: C 21 MET cc_start: 0.7959 (tpp) cc_final: 0.7043 (tpp) REVERT: C 40 ILE cc_start: 0.0136 (OUTLIER) cc_final: -0.0502 (mm) REVERT: D 348 ASN cc_start: 0.7448 (t0) cc_final: 0.6926 (t0) REVERT: E 349 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7504 (mp) REVERT: K 27 GLN cc_start: 0.8827 (mm110) cc_final: 0.8505 (tp-100) REVERT: a 281 MET cc_start: 0.1779 (tpt) cc_final: 0.0867 (mmm) REVERT: b 247 TRP cc_start: 0.5075 (OUTLIER) cc_final: 0.4173 (m-90) REVERT: g 258 LYS cc_start: 0.6579 (mmmt) cc_final: 0.6238 (mmmt) outliers start: 117 outliers final: 105 residues processed: 468 average time/residue: 0.5942 time to fit residues: 482.2960 Evaluate side-chains 485 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 376 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TRP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 362 TRP Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 92 SER Chi-restraints excluded: chain H residue 256 ASP Chi-restraints excluded: chain H residue 258 LYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 220 GLU Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 362 TRP Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 126 ILE Chi-restraints excluded: chain b residue 144 ILE Chi-restraints excluded: chain b residue 152 PHE Chi-restraints excluded: chain b residue 211 ASP Chi-restraints excluded: chain b residue 247 TRP Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 46 ASP Chi-restraints excluded: chain c residue 144 VAL Chi-restraints excluded: chain d residue 53 ASP Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 182 ASN Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 322 ASP Chi-restraints excluded: chain d residue 355 PHE Chi-restraints excluded: chain e residue 37 LEU Chi-restraints excluded: chain e residue 141 VAL Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 200 ILE Chi-restraints excluded: chain e residue 345 VAL Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 80 ASP Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain f residue 119 LEU Chi-restraints excluded: chain f residue 153 LEU Chi-restraints excluded: chain f residue 304 TYR Chi-restraints excluded: chain g residue 34 GLU Chi-restraints excluded: chain g residue 72 ILE Chi-restraints excluded: chain g residue 119 LEU Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain g residue 202 LEU Chi-restraints excluded: chain g residue 274 ILE Chi-restraints excluded: chain g residue 301 VAL Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 166 PHE Chi-restraints excluded: chain h residue 247 SER Chi-restraints excluded: chain h residue 350 ILE Chi-restraints excluded: chain i residue 62 THR Chi-restraints excluded: chain i residue 71 THR Chi-restraints excluded: chain i residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 5.9990 chunk 527 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 456 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 207 optimal weight: 0.5980 chunk 509 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 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 240 GLN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN ** a 255 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** b 306 HIS ** d 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.099617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072474 restraints weight = 236463.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074394 restraints weight = 114748.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075628 restraints weight = 71981.729| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 51920 Z= 0.220 Angle : 0.637 14.498 71122 Z= 0.316 Chirality : 0.041 0.269 8012 Planarity : 0.004 0.061 8928 Dihedral : 14.505 178.259 8708 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.27 % Allowed : 25.16 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 6192 helix: 1.43 (0.12), residues: 1944 sheet: 0.67 (0.17), residues: 966 loop : -1.21 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 394 HIS 0.009 0.001 HIS b 306 PHE 0.035 0.002 PHE F 195 TYR 0.020 0.002 TYR e 266 ARG 0.008 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11520.41 seconds wall clock time: 210 minutes 12.64 seconds (12612.64 seconds total)