Starting phenix.real_space_refine on Tue Mar 19 15:03:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzy_22584/03_2024/7jzy_22584.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 60 5.49 5 S 33 5.16 5 C 15198 2.51 5 N 4473 2.21 5 O 4775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 12": "OE1" <-> "OE2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ASP 133": "OD1" <-> "OD2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E ASP 334": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F ASP 130": "OD1" <-> "OD2" Residue "F ASP 135": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 240": "OD1" <-> "OD2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F ASP 270": "OD1" <-> "OD2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H ASP 204": "OD1" <-> "OD2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 270": "OD1" <-> "OD2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 292": "OD1" <-> "OD2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I ASP 130": "OD1" <-> "OD2" Residue "I TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 135": "OD1" <-> "OD2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I ASP 292": "OD1" <-> "OD2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I ASP 328": "OD1" <-> "OD2" Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 60": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3088 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 234 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: {'PCIS': 1, 'PTRANS': 14, '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: {'PCIS': 1, 'PTRANS': 14, '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: "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: "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: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 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: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "K" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 545 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Time building chain proxies: 13.14, per 1000 atoms: 0.54 Number of scatterers: 24539 At special positions: 0 Unit cell: (130.2, 157.5, 150.15, 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 33 16.00 P 60 15.00 O 4775 8.00 N 4473 7.00 C 15198 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: 9.56 Conformation dependent library (CDL) restraints added in 4.5 seconds 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5630 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 55 sheets defined 32.3% alpha, 21.4% beta 6 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.423A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.715A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.341A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.834A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.593A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 4.011A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.908A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.645A pdb=" N SER A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.885A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 3.599A pdb=" N ALA A 349 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.963A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.799A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 48 removed outlier: 3.864A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.542A pdb=" N ARG B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.888A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.857A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'C' and resid 16 through 36 removed outlier: 3.507A pdb=" N LEU C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.728A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'D' and resid 51 through 55 removed outlier: 3.621A pdb=" N SER D 55 " --> pdb=" O ARG D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 209 through 223 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 322 through 332 removed outlier: 3.646A pdb=" N LEU D 326 " --> pdb=" O ASP D 322 " (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 209 through 223 removed outlier: 3.510A pdb=" N ALA E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.523A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 332 removed outlier: 3.577A 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 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.652A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.506A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 removed outlier: 3.703A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 91 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 293 through 297 removed outlier: 3.644A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 332 removed outlier: 3.605A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'H' and resid 82 through 92 removed outlier: 3.575A pdb=" N SER H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 148 Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.506A pdb=" N ARG H 155 " --> pdb=" O ALA H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 removed outlier: 3.538A pdb=" N LEU H 326 " --> pdb=" O ASP H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.530A pdb=" N SER I 55 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 removed outlier: 3.578A pdb=" N LEU I 326 " --> pdb=" O ASP I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.584A pdb=" N ARG J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.584A pdb=" N ARG K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) 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 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.244A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.244A pdb=" N ALA A 191 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN B 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.518A pdb=" N PHE A 232 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.005A pdb=" N LEU A 265 " --> pdb=" O TRP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 60 removed outlier: 4.088A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.773A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AB2, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.547A pdb=" N SER B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB4, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'C' and resid 100 through 103 removed outlier: 4.192A pdb=" N PHE C 158 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.630A pdb=" N VAL D 118 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 179 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.707A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC4, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC5, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.742A pdb=" N ALA E 127 " --> pdb=" O ALA E 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.789A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.789A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.500A pdb=" N GLY E 70 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.113A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 306 through 307 removed outlier: 3.514A pdb=" N VAL E 307 " --> pdb=" O LYS E 312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 312 " --> pdb=" O VAL E 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.564A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.624A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.831A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL F 118 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 63 through 70 removed outlier: 3.799A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AD7, first strand: chain 'F' and resid 306 through 307 Processing sheet with id=AD8, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AD9, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.627A pdb=" N VAL G 118 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 189 through 192 removed outlier: 6.819A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 118 " --> pdb=" O VAL G 228 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 63 through 66 Processing sheet with id=AE3, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.504A pdb=" N GLY G 70 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 285 through 287 Processing sheet with id=AE5, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AE6, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE7, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.323A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 189 through 192 removed outlier: 6.810A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.614A pdb=" N GLY H 70 " --> pdb=" O ASN H 94 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AF2, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.783A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.611A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 32 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.741A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 189 through 192 removed outlier: 6.677A pdb=" N HIS I 183 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA I 192 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE I 181 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 64 through 70 removed outlier: 3.616A pdb=" N GLY I 70 " --> pdb=" O ASN I 94 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF8, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.656A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 20 through 24 removed outlier: 3.649A pdb=" N ALA J 56 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 20 through 24 removed outlier: 3.648A pdb=" N ALA K 56 " --> pdb=" O ILE K 47 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2883 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 8.48 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4773 1.32 - 1.45: 6345 1.45 - 1.57: 13855 1.57 - 1.69: 120 1.69 - 1.81: 50 Bond restraints: 25143 Sorted by residual: bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.385 -0.048 9.80e-03 1.04e+04 2.45e+01 bond pdb=" N ASP G 253 " pdb=" CA ASP G 253 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.05e+00 bond pdb=" CD LYS I 257 " pdb=" CE LYS I 257 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.32e+00 bond pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.83e+00 bond pdb=" N LEU C 71 " pdb=" CA LEU C 71 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.77e+00 ... (remaining 25138 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.50: 991 106.50 - 113.46: 13862 113.46 - 120.42: 9920 120.42 - 127.38: 9222 127.38 - 134.34: 420 Bond angle restraints: 34415 Sorted by residual: angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.82 129.53 -8.71 1.50e+00 4.44e-01 3.37e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C LEU A 32 " pdb=" N GLN A 33 " pdb=" CA GLN A 33 " ideal model delta sigma weight residual 123.10 127.51 -4.41 9.60e-01 1.09e+00 2.11e+01 angle pdb=" C LYS F 77 " pdb=" N THR F 78 " pdb=" CA THR F 78 " ideal model delta sigma weight residual 121.54 129.90 -8.36 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C4' C M 37 " pdb=" C3' C M 37 " pdb=" O3' C M 37 " ideal model delta sigma weight residual 109.40 115.95 -6.55 1.50e+00 4.44e-01 1.91e+01 ... (remaining 34410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 14655 35.34 - 70.67: 492 70.67 - 106.01: 49 106.01 - 141.34: 1 141.34 - 176.68: 6 Dihedral angle restraints: 15203 sinusoidal: 6493 harmonic: 8710 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 44.21 155.79 1 1.50e+01 4.44e-03 8.16e+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 45.69 154.31 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual -128.00 48.68 -176.68 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3421 0.079 - 0.158: 431 0.158 - 0.236: 30 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 3885 Sorted by residual: chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.07 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' A M 36 " pdb=" C4' A M 36 " pdb=" O3' A M 36 " pdb=" C2' A M 36 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3882 not shown) Planarity restraints: 4315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 186 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN D 186 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN D 186 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY D 187 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 300 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C ASP B 300 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP B 300 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 301 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 72 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.041 5.00e-02 4.00e+02 ... (remaining 4312 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5173 2.77 - 3.30: 21534 3.30 - 3.83: 41266 3.83 - 4.37: 48830 4.37 - 4.90: 82946 Nonbonded interactions: 199749 Sorted by model distance: nonbonded pdb=" OH TYR E 324 " pdb=" O SER F 73 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.250 2.440 nonbonded pdb=" OG SER B 24 " pdb=" O PHE B 31 " model vdw 2.252 2.440 nonbonded pdb=" O2' C M 31 " pdb=" O ARG F 69 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR D 324 " pdb=" O SER E 73 " model vdw 2.265 2.440 ... (remaining 199744 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 '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' } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.020 Extract box with map and model: 5.220 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 67.550 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.009 0.081 25143 Z= 0.579 Angle : 0.960 10.568 34415 Z= 0.544 Chirality : 0.053 0.394 3885 Planarity : 0.006 0.072 4315 Dihedral : 17.371 176.679 9573 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.85 % Allowed : 10.25 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -3.78 (0.12), residues: 2995 helix: -2.61 (0.12), residues: 902 sheet: -1.18 (0.22), residues: 482 loop : -2.95 (0.12), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 414 HIS 0.011 0.002 HIS D 343 PHE 0.026 0.002 PHE A 287 TYR 0.018 0.003 TYR E 290 ARG 0.026 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 418 time to evaluate : 2.655 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: A 216 LYS cc_start: 0.8820 (tppt) cc_final: 0.8054 (pttp) REVERT: B 124 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7625 (pm20) REVERT: D 146 ASN cc_start: 0.8180 (t0) cc_final: 0.7814 (t0) REVERT: D 159 HIS cc_start: 0.7826 (m90) cc_final: 0.7611 (m-70) REVERT: D 195 PHE cc_start: 0.8131 (m-80) cc_final: 0.7864 (m-80) REVERT: D 206 LYS cc_start: 0.7649 (tptt) cc_final: 0.7307 (tptp) REVERT: D 278 LYS cc_start: 0.8863 (tttp) cc_final: 0.8598 (tttt) REVERT: D 294 ASP cc_start: 0.7455 (t70) cc_final: 0.7211 (t70) REVERT: E 74 ASN cc_start: 0.8420 (p0) cc_final: 0.7917 (p0) REVERT: E 146 ASN cc_start: 0.8863 (t0) cc_final: 0.8590 (t0) REVERT: F 90 ILE cc_start: 0.9164 (pt) cc_final: 0.8851 (mt) REVERT: F 94 ASN cc_start: 0.8581 (p0) cc_final: 0.8340 (p0) REVERT: F 203 ARG cc_start: 0.7593 (ptp-110) cc_final: 0.7257 (ttm110) REVERT: F 212 ASP cc_start: 0.8083 (m-30) cc_final: 0.7844 (m-30) REVERT: G 290 TYR cc_start: 0.8867 (p90) cc_final: 0.8654 (p90) REVERT: H 146 ASN cc_start: 0.8273 (t0) cc_final: 0.7905 (t0) REVERT: H 251 ILE cc_start: 0.8545 (pt) cc_final: 0.8329 (pt) REVERT: H 269 ARG cc_start: 0.8549 (ptp-170) cc_final: 0.8274 (ptp90) REVERT: I 249 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7625 (mm-30) REVERT: I 312 LYS cc_start: 0.8754 (tttm) cc_final: 0.8393 (ttpp) REVERT: J 29 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: K 58 LYS cc_start: 0.9313 (tttm) cc_final: 0.8779 (tttp) outliers start: 20 outliers final: 5 residues processed: 430 average time/residue: 0.4474 time to fit residues: 279.6427 Evaluate side-chains 268 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 306 HIS C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 ASN F 56 GLN F 183 HIS F 242 GLN F 281 ASN G 51 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 GLN ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 310 GLN J 51 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25143 Z= 0.213 Angle : 0.586 10.919 34415 Z= 0.308 Chirality : 0.040 0.268 3885 Planarity : 0.004 0.059 4315 Dihedral : 15.136 179.320 4249 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.05 % Allowed : 14.99 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -2.37 (0.13), residues: 2995 helix: -0.50 (0.16), residues: 897 sheet: -0.77 (0.22), residues: 497 loop : -2.57 (0.13), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 394 HIS 0.006 0.001 HIS D 159 PHE 0.021 0.001 PHE C 173 TYR 0.017 0.001 TYR I 144 ARG 0.006 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 310 time to evaluate : 2.826 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: A 116 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7923 (p0) REVERT: A 332 GLU cc_start: 0.8085 (tp30) cc_final: 0.7877 (tt0) REVERT: A 417 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7617 (pt0) REVERT: B 124 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7622 (pm20) REVERT: C 186 TRP cc_start: 0.7944 (t-100) cc_final: 0.7664 (t-100) REVERT: D 146 ASN cc_start: 0.8205 (t0) cc_final: 0.7871 (t0) REVERT: D 195 PHE cc_start: 0.8062 (m-80) cc_final: 0.7768 (m-80) REVERT: D 206 LYS cc_start: 0.7829 (tptt) cc_final: 0.7499 (tptp) REVERT: D 211 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8620 (tt) REVERT: D 212 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: D 294 ASP cc_start: 0.7456 (t70) cc_final: 0.7159 (t70) REVERT: D 312 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7873 (ttpp) REVERT: E 74 ASN cc_start: 0.8286 (p0) cc_final: 0.7856 (p0) REVERT: E 146 ASN cc_start: 0.8896 (t0) cc_final: 0.8655 (t0) REVERT: F 203 ARG cc_start: 0.7533 (ptp-110) cc_final: 0.7160 (ttm110) REVERT: G 155 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7658 (ttp80) REVERT: H 269 ARG cc_start: 0.8557 (ptp-170) cc_final: 0.8305 (ptp90) REVERT: H 304 TYR cc_start: 0.8322 (m-80) cc_final: 0.8051 (m-80) REVERT: I 249 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7620 (mm-30) REVERT: I 310 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: I 321 LEU cc_start: 0.8296 (mt) cc_final: 0.7766 (mp) REVERT: J 29 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: K 58 LYS cc_start: 0.9094 (tttm) cc_final: 0.8486 (tttp) outliers start: 48 outliers final: 28 residues processed: 344 average time/residue: 0.3796 time to fit residues: 198.7836 Evaluate side-chains 306 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 310 GLN Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 272 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 220 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 203 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN B 306 HIS C 29 HIS C 165 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 GLN F 242 GLN F 260 GLN F 342 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 96 GLN I 148 GLN ** I 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 310 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25143 Z= 0.207 Angle : 0.553 12.914 34415 Z= 0.288 Chirality : 0.040 0.247 3885 Planarity : 0.004 0.050 4315 Dihedral : 14.988 178.752 4247 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.29 % Allowed : 16.79 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -1.67 (0.14), residues: 2995 helix: 0.47 (0.17), residues: 901 sheet: -0.55 (0.22), residues: 502 loop : -2.34 (0.13), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 330 HIS 0.005 0.001 HIS D 343 PHE 0.012 0.001 PHE G 114 TYR 0.013 0.001 TYR A 235 ARG 0.005 0.000 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 299 time to evaluate : 2.558 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: A 116 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8041 (p0) REVERT: A 332 GLU cc_start: 0.8117 (tp30) cc_final: 0.7864 (tt0) REVERT: B 124 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7607 (pm20) REVERT: C 186 TRP cc_start: 0.7911 (t-100) cc_final: 0.7608 (t-100) REVERT: D 146 ASN cc_start: 0.8224 (t0) cc_final: 0.7902 (t0) REVERT: D 195 PHE cc_start: 0.8062 (m-80) cc_final: 0.7773 (m-80) REVERT: D 206 LYS cc_start: 0.7541 (tptt) cc_final: 0.7253 (tptp) REVERT: D 211 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (tt) REVERT: D 212 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: D 294 ASP cc_start: 0.7595 (t70) cc_final: 0.7261 (t70) REVERT: D 312 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7815 (ttpp) REVERT: E 74 ASN cc_start: 0.8318 (p0) cc_final: 0.7870 (p0) REVERT: E 146 ASN cc_start: 0.8898 (t0) cc_final: 0.8666 (t0) REVERT: F 203 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7154 (ttm110) REVERT: H 146 ASN cc_start: 0.8298 (t0) cc_final: 0.7956 (t0) REVERT: H 269 ARG cc_start: 0.8559 (ptp-170) cc_final: 0.8306 (ptp90) REVERT: H 304 TYR cc_start: 0.8354 (m-80) cc_final: 0.8021 (m-80) REVERT: I 249 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7612 (mm-30) REVERT: I 277 GLN cc_start: 0.9127 (pm20) cc_final: 0.8866 (pt0) REVERT: I 290 TYR cc_start: 0.8178 (p90) cc_final: 0.7652 (p90) REVERT: I 321 LEU cc_start: 0.8376 (mt) cc_final: 0.7862 (mp) REVERT: J 29 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: K 6 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.7917 (mp) outliers start: 77 outliers final: 50 residues processed: 357 average time/residue: 0.3887 time to fit residues: 212.3098 Evaluate side-chains 320 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 312 LYS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 29 GLN Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 291 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN F 242 GLN F 260 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 ASN I 159 HIS I 342 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25143 Z= 0.180 Angle : 0.535 12.447 34415 Z= 0.277 Chirality : 0.039 0.288 3885 Planarity : 0.003 0.048 4315 Dihedral : 14.861 177.624 4247 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.99 % Allowed : 17.81 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -1.28 (0.15), residues: 2995 helix: 0.96 (0.17), residues: 908 sheet: -0.40 (0.22), residues: 499 loop : -2.20 (0.14), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 394 HIS 0.004 0.001 HIS B 293 PHE 0.023 0.001 PHE A 425 TYR 0.013 0.001 TYR H 133 ARG 0.005 0.000 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 300 time to evaluate : 2.678 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: A 332 GLU cc_start: 0.7987 (tp30) cc_final: 0.7751 (tt0) REVERT: B 124 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7570 (pm20) REVERT: C 117 MET cc_start: 0.4006 (mmp) cc_final: 0.3779 (mtp) REVERT: C 186 TRP cc_start: 0.7958 (t-100) cc_final: 0.7676 (t-100) REVERT: D 146 ASN cc_start: 0.8303 (t0) cc_final: 0.7976 (t0) REVERT: D 195 PHE cc_start: 0.7943 (m-80) cc_final: 0.7667 (m-80) REVERT: D 294 ASP cc_start: 0.7666 (t70) cc_final: 0.7313 (t70) REVERT: E 74 ASN cc_start: 0.8309 (p0) cc_final: 0.7864 (p0) REVERT: E 146 ASN cc_start: 0.8882 (t0) cc_final: 0.8653 (t0) REVERT: F 203 ARG cc_start: 0.7578 (ptp-110) cc_final: 0.7189 (ttm110) REVERT: H 146 ASN cc_start: 0.8274 (t0) cc_final: 0.7937 (t0) REVERT: H 211 LEU cc_start: 0.8497 (mt) cc_final: 0.8209 (tt) REVERT: H 269 ARG cc_start: 0.8542 (ptp-170) cc_final: 0.8303 (ptp90) REVERT: H 304 TYR cc_start: 0.8326 (m-80) cc_final: 0.7942 (m-80) REVERT: I 249 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7661 (mm-30) REVERT: I 277 GLN cc_start: 0.9081 (pm20) cc_final: 0.8853 (pt0) REVERT: I 290 TYR cc_start: 0.8118 (p90) cc_final: 0.7767 (p90) REVERT: I 321 LEU cc_start: 0.8400 (mt) cc_final: 0.7960 (mp) REVERT: K 6 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8001 (mp) outliers start: 70 outliers final: 50 residues processed: 352 average time/residue: 0.3895 time to fit residues: 211.5786 Evaluate side-chains 329 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 278 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 50 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 120 optimal weight: 0.0670 chunk 249 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 149 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 396 ASN C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25143 Z= 0.168 Angle : 0.524 11.686 34415 Z= 0.270 Chirality : 0.039 0.241 3885 Planarity : 0.003 0.049 4315 Dihedral : 14.726 177.469 4244 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.16 % Allowed : 18.11 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.96 (0.15), residues: 2995 helix: 1.32 (0.17), residues: 911 sheet: -0.19 (0.23), residues: 487 loop : -2.07 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 394 HIS 0.008 0.001 HIS D 159 PHE 0.011 0.001 PHE A 425 TYR 0.018 0.001 TYR A 235 ARG 0.005 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 295 time to evaluate : 2.445 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: A 414 TRP cc_start: 0.6509 (t60) cc_final: 0.5991 (t60) REVERT: B 124 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7565 (pm20) REVERT: C 117 MET cc_start: 0.4064 (mmp) cc_final: 0.3822 (mtp) REVERT: C 186 TRP cc_start: 0.7874 (t-100) cc_final: 0.7634 (t-100) REVERT: D 146 ASN cc_start: 0.8242 (t0) cc_final: 0.7930 (t0) REVERT: D 195 PHE cc_start: 0.7826 (m-80) cc_final: 0.7578 (m-80) REVERT: D 294 ASP cc_start: 0.7668 (t70) cc_final: 0.7274 (t70) REVERT: E 74 ASN cc_start: 0.8282 (p0) cc_final: 0.7843 (p0) REVERT: E 146 ASN cc_start: 0.8883 (t0) cc_final: 0.8665 (t0) REVERT: F 203 ARG cc_start: 0.7545 (ptp-110) cc_final: 0.7111 (ttm110) REVERT: H 211 LEU cc_start: 0.8490 (mt) cc_final: 0.8227 (tt) REVERT: H 269 ARG cc_start: 0.8529 (ptp-170) cc_final: 0.8289 (ptp90) REVERT: H 304 TYR cc_start: 0.8291 (m-80) cc_final: 0.7961 (m-80) REVERT: H 321 LEU cc_start: 0.8560 (tp) cc_final: 0.8323 (tp) REVERT: I 249 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7729 (mm-30) REVERT: I 277 GLN cc_start: 0.9109 (pm20) cc_final: 0.8892 (pt0) REVERT: I 290 TYR cc_start: 0.8113 (p90) cc_final: 0.7753 (p90) REVERT: I 321 LEU cc_start: 0.8416 (mt) cc_final: 0.7960 (mp) REVERT: J 36 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8575 (tttm) outliers start: 74 outliers final: 48 residues processed: 347 average time/residue: 0.3688 time to fit residues: 197.1273 Evaluate side-chains 325 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 242 GLN F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25143 Z= 0.341 Angle : 0.607 12.343 34415 Z= 0.311 Chirality : 0.041 0.232 3885 Planarity : 0.004 0.051 4315 Dihedral : 14.762 177.912 4243 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.33 % Allowed : 18.92 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.99 (0.15), residues: 2995 helix: 1.29 (0.17), residues: 907 sheet: -0.14 (0.23), residues: 492 loop : -2.11 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 394 HIS 0.006 0.001 HIS D 343 PHE 0.016 0.002 PHE F 114 TYR 0.014 0.002 TYR G 290 ARG 0.007 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 275 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7716 (pt0) REVERT: B 82 ASN cc_start: 0.9362 (m-40) cc_final: 0.9060 (m-40) REVERT: C 56 GLU cc_start: 0.6284 (tp30) cc_final: 0.6078 (tp30) REVERT: C 186 TRP cc_start: 0.7988 (t-100) cc_final: 0.7607 (t-100) REVERT: D 146 ASN cc_start: 0.8140 (t0) cc_final: 0.7824 (t0) REVERT: D 195 PHE cc_start: 0.7939 (m-80) cc_final: 0.7620 (m-80) REVERT: D 212 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: D 294 ASP cc_start: 0.7672 (t70) cc_final: 0.7296 (t70) REVERT: E 74 ASN cc_start: 0.8273 (p0) cc_final: 0.7851 (p0) REVERT: E 96 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: E 146 ASN cc_start: 0.8980 (t0) cc_final: 0.8760 (t0) REVERT: F 203 ARG cc_start: 0.7677 (ptp-110) cc_final: 0.7174 (ttm110) REVERT: F 249 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: H 146 ASN cc_start: 0.8401 (t0) cc_final: 0.8054 (t0) REVERT: H 269 ARG cc_start: 0.8601 (ptp-170) cc_final: 0.8348 (ptp90) REVERT: H 339 VAL cc_start: 0.8237 (t) cc_final: 0.7920 (p) REVERT: I 249 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7665 (mm-30) REVERT: I 277 GLN cc_start: 0.9171 (pm20) cc_final: 0.8705 (pt0) REVERT: I 290 TYR cc_start: 0.8213 (p90) cc_final: 0.7869 (p90) REVERT: I 321 LEU cc_start: 0.8501 (mt) cc_final: 0.7961 (mp) REVERT: J 36 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8540 (tttm) REVERT: J 63 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7444 (mmm160) REVERT: K 6 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.7993 (mp) REVERT: K 47 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8015 (mm) outliers start: 78 outliers final: 56 residues processed: 334 average time/residue: 0.3636 time to fit residues: 189.6118 Evaluate side-chains 323 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 262 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 291 optimal weight: 0.4980 chunk 182 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN B 306 HIS C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 342 GLN F 242 GLN F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25143 Z= 0.162 Angle : 0.529 12.089 34415 Z= 0.271 Chirality : 0.039 0.222 3885 Planarity : 0.003 0.051 4315 Dihedral : 14.698 177.235 4243 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.16 % Allowed : 19.56 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.72 (0.15), residues: 2995 helix: 1.63 (0.17), residues: 906 sheet: -0.06 (0.23), residues: 486 loop : -1.98 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 394 HIS 0.004 0.001 HIS B 306 PHE 0.009 0.001 PHE H 166 TYR 0.016 0.001 TYR A 235 ARG 0.006 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 289 time to evaluate : 2.732 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: B 281 GLU cc_start: 0.7974 (pp20) cc_final: 0.7444 (pp20) REVERT: C 1 MET cc_start: 0.4777 (mmt) cc_final: 0.4557 (mmt) REVERT: C 56 GLU cc_start: 0.6028 (tp30) cc_final: 0.5807 (tp30) REVERT: C 186 TRP cc_start: 0.7944 (t-100) cc_final: 0.7601 (t-100) REVERT: D 146 ASN cc_start: 0.8181 (t0) cc_final: 0.7850 (t0) REVERT: D 159 HIS cc_start: 0.8072 (m-70) cc_final: 0.7797 (m170) REVERT: D 195 PHE cc_start: 0.7870 (m-80) cc_final: 0.7587 (m-80) REVERT: D 294 ASP cc_start: 0.7665 (t70) cc_final: 0.7348 (t70) REVERT: E 74 ASN cc_start: 0.8290 (p0) cc_final: 0.7917 (p0) REVERT: E 146 ASN cc_start: 0.8928 (t0) cc_final: 0.8716 (t0) REVERT: E 348 ASN cc_start: 0.9029 (t0) cc_final: 0.8590 (t0) REVERT: F 203 ARG cc_start: 0.7517 (ptp-110) cc_final: 0.7015 (ttm110) REVERT: H 146 ASN cc_start: 0.8299 (t0) cc_final: 0.7881 (t0) REVERT: H 211 LEU cc_start: 0.8529 (mt) cc_final: 0.8304 (tt) REVERT: H 269 ARG cc_start: 0.8542 (ptp-170) cc_final: 0.8320 (ptp90) REVERT: I 249 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7703 (mm-30) REVERT: I 290 TYR cc_start: 0.8178 (p90) cc_final: 0.7806 (p90) REVERT: I 321 LEU cc_start: 0.8444 (mt) cc_final: 0.7992 (mp) REVERT: I 333 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8031 (mtt90) REVERT: K 47 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7959 (mm) outliers start: 74 outliers final: 55 residues processed: 341 average time/residue: 0.3726 time to fit residues: 198.0514 Evaluate side-chains 324 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 267 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 56 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25143 Z= 0.197 Angle : 0.544 12.508 34415 Z= 0.277 Chirality : 0.039 0.240 3885 Planarity : 0.003 0.051 4315 Dihedral : 14.651 177.232 4243 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.78 % Allowed : 20.38 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.68 (0.15), residues: 2995 helix: 1.64 (0.17), residues: 913 sheet: -0.01 (0.24), residues: 484 loop : -1.96 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 394 HIS 0.004 0.001 HIS B 305 PHE 0.014 0.001 PHE A 391 TYR 0.019 0.001 TYR C 97 ARG 0.007 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 274 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.4777 (mmt) cc_final: 0.4560 (mmt) REVERT: C 14 GLU cc_start: 0.7815 (mp0) cc_final: 0.7518 (mm-30) REVERT: D 146 ASN cc_start: 0.8138 (t0) cc_final: 0.7823 (t0) REVERT: D 195 PHE cc_start: 0.7951 (m-80) cc_final: 0.7648 (m-80) REVERT: D 212 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: D 294 ASP cc_start: 0.7645 (t70) cc_final: 0.7334 (t70) REVERT: E 74 ASN cc_start: 0.8276 (p0) cc_final: 0.7912 (p0) REVERT: E 146 ASN cc_start: 0.8920 (t0) cc_final: 0.8715 (t0) REVERT: E 348 ASN cc_start: 0.9072 (t0) cc_final: 0.8499 (t0) REVERT: F 203 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.7001 (ttm110) REVERT: G 73 SER cc_start: 0.8475 (t) cc_final: 0.8030 (t) REVERT: H 146 ASN cc_start: 0.8310 (t0) cc_final: 0.7893 (t0) REVERT: H 321 LEU cc_start: 0.8517 (tp) cc_final: 0.8274 (tp) REVERT: H 339 VAL cc_start: 0.8183 (t) cc_final: 0.7870 (p) REVERT: I 249 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7745 (mm-30) REVERT: I 290 TYR cc_start: 0.8175 (p90) cc_final: 0.7753 (p90) REVERT: I 321 LEU cc_start: 0.8447 (mt) cc_final: 0.8007 (mp) REVERT: I 333 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8035 (mtt90) REVERT: K 6 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.7934 (mp) REVERT: K 47 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7952 (mm) outliers start: 65 outliers final: 57 residues processed: 315 average time/residue: 0.3725 time to fit residues: 181.1835 Evaluate side-chains 326 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 414 TRP Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 256 optimal weight: 0.6980 chunk 270 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 HIS F 242 GLN F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25143 Z= 0.243 Angle : 0.567 13.849 34415 Z= 0.288 Chirality : 0.040 0.233 3885 Planarity : 0.003 0.051 4315 Dihedral : 14.655 177.560 4243 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.16 % Allowed : 19.95 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % 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: -0.70 (0.15), residues: 2995 helix: 1.61 (0.17), residues: 913 sheet: -0.02 (0.24), residues: 484 loop : -1.97 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 394 HIS 0.005 0.001 HIS B 305 PHE 0.013 0.001 PHE G 114 TYR 0.022 0.002 TYR I 144 ARG 0.007 0.000 ARG J 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 273 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7518 (t0) cc_final: 0.7179 (t70) REVERT: A 235 TYR cc_start: 0.8662 (m-80) cc_final: 0.8422 (m-80) REVERT: A 287 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5671 (t80) REVERT: D 146 ASN cc_start: 0.8150 (t0) cc_final: 0.7841 (t0) REVERT: D 195 PHE cc_start: 0.7926 (m-80) cc_final: 0.7616 (m-80) REVERT: D 212 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: D 294 ASP cc_start: 0.7629 (t70) cc_final: 0.7317 (t0) REVERT: D 312 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7929 (ttpp) REVERT: E 74 ASN cc_start: 0.8283 (p0) cc_final: 0.7914 (p0) REVERT: E 146 ASN cc_start: 0.8944 (t0) cc_final: 0.8737 (t0) REVERT: E 348 ASN cc_start: 0.9106 (t0) cc_final: 0.8494 (t0) REVERT: F 203 ARG cc_start: 0.7564 (ptp-110) cc_final: 0.7034 (ttm110) REVERT: F 249 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: F 348 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8875 (t0) REVERT: G 73 SER cc_start: 0.8571 (t) cc_final: 0.8123 (t) REVERT: H 79 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8414 (mmmm) REVERT: H 146 ASN cc_start: 0.8330 (t0) cc_final: 0.7923 (t0) REVERT: H 321 LEU cc_start: 0.8576 (tp) cc_final: 0.8324 (tp) REVERT: H 339 VAL cc_start: 0.8204 (t) cc_final: 0.7885 (p) REVERT: I 249 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7722 (mm-30) REVERT: I 290 TYR cc_start: 0.8181 (p90) cc_final: 0.7780 (p90) REVERT: I 321 LEU cc_start: 0.8484 (mt) cc_final: 0.7974 (mp) REVERT: I 333 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8083 (mtt90) REVERT: K 6 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.7951 (mp) REVERT: K 47 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7956 (mm) outliers start: 74 outliers final: 59 residues processed: 324 average time/residue: 0.3702 time to fit residues: 185.3745 Evaluate side-chains 329 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 199 optimal weight: 0.4980 chunk 300 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 185 optimal weight: 0.3980 chunk 146 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 25143 Z= 0.237 Angle : 0.703 59.197 34415 Z= 0.384 Chirality : 0.040 0.585 3885 Planarity : 0.003 0.051 4315 Dihedral : 14.656 177.555 4243 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.82 % Allowed : 20.67 % Favored : 76.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.75 % 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: -0.68 (0.15), residues: 2995 helix: 1.65 (0.17), residues: 913 sheet: -0.02 (0.24), residues: 484 loop : -1.96 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 394 HIS 0.005 0.001 HIS H 275 PHE 0.012 0.001 PHE F 114 TYR 0.023 0.002 TYR I 144 ARG 0.006 0.000 ARG G 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5990 Ramachandran restraints generated. 2995 Oldfield, 0 Emsley, 2995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7503 (t0) cc_final: 0.7168 (t70) REVERT: A 235 TYR cc_start: 0.8660 (m-80) cc_final: 0.8414 (m-80) REVERT: A 287 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5667 (t80) REVERT: D 146 ASN cc_start: 0.8148 (t0) cc_final: 0.7840 (t0) REVERT: D 195 PHE cc_start: 0.7922 (m-80) cc_final: 0.7613 (m-80) REVERT: D 212 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: D 294 ASP cc_start: 0.7625 (t70) cc_final: 0.7323 (t0) REVERT: E 74 ASN cc_start: 0.8277 (p0) cc_final: 0.7913 (p0) REVERT: E 146 ASN cc_start: 0.8941 (t0) cc_final: 0.8735 (t0) REVERT: E 348 ASN cc_start: 0.9101 (t0) cc_final: 0.8492 (t0) REVERT: F 203 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7028 (ttm110) REVERT: F 249 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: F 348 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8874 (t0) REVERT: G 73 SER cc_start: 0.8568 (t) cc_final: 0.8117 (t) REVERT: H 79 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8413 (mmmm) REVERT: H 146 ASN cc_start: 0.8329 (t0) cc_final: 0.7919 (t0) REVERT: H 321 LEU cc_start: 0.8589 (tp) cc_final: 0.8332 (tp) REVERT: H 339 VAL cc_start: 0.8200 (t) cc_final: 0.7882 (p) REVERT: I 249 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7722 (mm-30) REVERT: I 290 TYR cc_start: 0.8186 (p90) cc_final: 0.7775 (p90) REVERT: I 321 LEU cc_start: 0.8488 (mt) cc_final: 0.7973 (mp) REVERT: I 333 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8079 (mtt90) REVERT: K 6 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.7948 (mp) REVERT: K 47 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (mm) outliers start: 66 outliers final: 58 residues processed: 310 average time/residue: 0.3742 time to fit residues: 180.2185 Evaluate side-chains 326 residues out of total 2448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 270 ASP Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 51 GLN Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 270 ASP Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 308 THR Chi-restraints excluded: chain H residue 331 VAL Chi-restraints excluded: chain H residue 348 ASN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 252 LEU Chi-restraints excluded: chain I residue 304 TYR Chi-restraints excluded: chain I residue 333 ARG Chi-restraints excluded: chain I residue 334 ASP Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain K residue 6 ILE Chi-restraints excluded: chain K residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 2.9990 chunk 255 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN F 310 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.101748 restraints weight = 47767.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.100549 restraints weight = 33308.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100800 restraints weight = 41467.133| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.177 25143 Z= 0.237 Angle : 0.703 59.197 34415 Z= 0.384 Chirality : 0.040 0.585 3885 Planarity : 0.003 0.051 4315 Dihedral : 14.656 177.555 4243 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.78 % Allowed : 20.72 % Favored : 76.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.75 % 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: -0.68 (0.15), residues: 2995 helix: 1.65 (0.17), residues: 913 sheet: -0.02 (0.24), residues: 484 loop : -1.96 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 394 HIS 0.005 0.001 HIS H 275 PHE 0.012 0.001 PHE F 114 TYR 0.023 0.002 TYR I 144 ARG 0.006 0.000 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.41 seconds wall clock time: 86 minutes 19.09 seconds (5179.09 seconds total)