Starting phenix.real_space_refine on Tue Mar 19 15:13:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhs_33837/03_2024/7yhs_33837.pdb" } resolution = 3.37 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= 0.004 sd= 0.042 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 108 5.49 5 S 25 5.16 5 C 15076 2.51 5 N 4520 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 55": "OD1" <-> "OD2" 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 220": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 208": "OD1" <-> "OD2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 357": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 108": "OD1" <-> "OD2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "G ASP 322": "OD1" <-> "OD2" Residue "G ASP 328": "OD1" <-> "OD2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H ASP 196": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 196": "OD1" <-> "OD2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ASP 328": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "L ASP 12": "OD1" <-> "OD2" Residue "L ASP 38": "OD1" <-> "OD2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 126": "OE1" <-> "OE2" 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: 24596 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3039 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 24, 'TRANS': 398} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 480 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 256 Chain: "C" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2240 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2425 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "E" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2373 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2548 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2529 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "H" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2490 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2514 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "L" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1428 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "M" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1226 Classifications: {'RNA': 58} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 18, 'rna3p_pur': 14, 'rna3p_pyr': 13} Link IDs: {'rna2p': 29, 'rna3p': 28} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 803 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 244 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 13.50, per 1000 atoms: 0.55 Number of scatterers: 24596 At special positions: 0 Unit cell: (148.41, 138.71, 181.39, 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 25 16.00 P 108 15.00 O 4867 8.00 N 4520 7.00 C 15076 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: 9.16 Conformation dependent library (CDL) restraints added in 4.0 seconds 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 40 sheets defined 30.7% alpha, 17.8% beta 31 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 8.17 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.159A pdb=" N PHE A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 4.325A pdb=" N LEU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 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: 4.083A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.752A pdb=" N GLN A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.625A pdb=" N ARG A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.554A pdb=" N ALA A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.896A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.668A pdb=" N LEU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.731A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.842A pdb=" N TRP A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 374 through 382 removed outlier: 4.174A pdb=" N ARG A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.912A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 148 removed outlier: 3.596A pdb=" N ARG C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.727A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 3.571A pdb=" N ALA C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 339 through 352 Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.849A pdb=" N ARG D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 Processing helix chain 'D' and resid 208 through 223 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.734A pdb=" N ILE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 33 through 48 removed outlier: 3.902A pdb=" N PHE E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 135 removed outlier: 3.508A pdb=" N GLY E 135 " --> pdb=" O GLN E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.954A pdb=" N LEU E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 removed outlier: 3.617A pdb=" N ALA E 212 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 214 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 removed outlier: 3.734A pdb=" N ARG F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.646A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 224 Processing helix chain 'F' and resid 275 through 284 removed outlier: 3.603A pdb=" N ILE F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 331 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.536A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) 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: 3.786A pdb=" N LEU G 296 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY G 297 " --> pdb=" O ASP G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 293 through 297' Processing helix chain 'G' and resid 322 through 331 removed outlier: 3.631A 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 86 through 91 removed outlier: 3.911A pdb=" N ILE H 90 " --> pdb=" O LEU H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 224 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 82 through 92 removed outlier: 3.675A pdb=" N LEU I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 148 removed outlier: 3.772A pdb=" N ARG I 134 " --> pdb=" O ASP I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 163 Processing helix chain 'I' and resid 208 through 222 Processing helix chain 'I' and resid 275 through 283 removed outlier: 3.658A pdb=" N ILE I 279 " --> pdb=" O HIS I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 297 removed outlier: 3.535A pdb=" N LEU I 296 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY I 297 " --> pdb=" O ASP I 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 293 through 297' Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 removed outlier: 3.577A pdb=" N GLN I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 removed outlier: 4.116A pdb=" N TYR J 12 " --> pdb=" O ASP J 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 78 Processing helix chain 'J' and resid 79 through 100 removed outlier: 3.659A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 97 " --> pdb=" O ALA J 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 27 Processing helix chain 'L' and resid 108 through 118 removed outlier: 4.474A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 6.432A pdb=" N ALA A 191 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASN E 282 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE E 279 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA E 257 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU E 281 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 255 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU E 283 " --> pdb=" O ALA E 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA5, first strand: chain 'C' and resid 31 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 191 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 45 removed outlier: 4.285A pdb=" N VAL C 228 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 229 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 176 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 128 removed outlier: 4.044A pdb=" N ALA D 127 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AB2, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.878A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU D 229 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 184 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA D 176 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 63 through 70 Processing sheet with id=AB4, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.737A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 56 through 61 removed outlier: 5.411A pdb=" N GLY E 58 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 110 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA E 103 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLN E 18 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 105 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E 16 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL E 107 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG E 14 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB8, first strand: chain 'E' and resid 304 through 306 Processing sheet with id=AB9, first strand: chain 'F' and resid 127 through 128 removed outlier: 3.709A pdb=" N ALA F 127 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 38 through 39 removed outlier: 3.890A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG F 191 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 38 through 39 removed outlier: 5.033A pdb=" N ALA F 272 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 64 through 70 Processing sheet with id=AC4, first strand: chain 'F' and resid 285 through 287 Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AC6, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG G 191 " --> pdb=" O HIS G 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 38 through 39 removed outlier: 3.542A pdb=" N ARG G 117 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 64 through 70 Processing sheet with id=AC9, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD1, first strand: chain 'H' and resid 127 through 128 removed outlier: 3.868A pdb=" N ALA H 127 " --> pdb=" O ALA H 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.987A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG H 191 " --> pdb=" O HIS H 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AD4, first strand: chain 'H' and resid 63 through 68 Processing sheet with id=AD5, first strand: chain 'H' and resid 285 through 287 Processing sheet with id=AD6, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.630A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.897A pdb=" N ALA I 127 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 32 " --> pdb=" O ALA I 127 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 189 through 196 removed outlier: 3.912A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA I 42 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 274 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ALA I 272 " --> pdb=" O MET I 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 64 through 70 Processing sheet with id=AE1, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AE2, first strand: chain 'J' and resid 17 through 21 Processing sheet with id=AE3, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.541A pdb=" N LEU L 58 " --> pdb=" O ILE L 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 100 through 103 removed outlier: 3.803A pdb=" N PHE L 158 " --> pdb=" O VAL L 103 " (cutoff:3.500A) 887 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3968 1.31 - 1.44: 7269 1.44 - 1.56: 13804 1.56 - 1.69: 216 1.69 - 1.81: 39 Bond restraints: 25296 Sorted by residual: bond pdb=" C PRO L 13 " pdb=" O PRO L 13 " ideal model delta sigma weight residual 1.239 1.187 0.052 1.22e-02 6.72e+03 1.82e+01 bond pdb=" N GLN L 35 " pdb=" CA GLN L 35 " ideal model delta sigma weight residual 1.457 1.482 -0.026 6.40e-03 2.44e+04 1.62e+01 bond pdb=" N ILE L 40 " pdb=" CA ILE L 40 " ideal model delta sigma weight residual 1.458 1.501 -0.044 1.14e-02 7.69e+03 1.47e+01 bond pdb=" C PRO A 229 " pdb=" O PRO A 229 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" N GLY L 36 " pdb=" CA GLY L 36 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.03e+01 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.56: 929 105.56 - 113.09: 13674 113.09 - 120.62: 10893 120.62 - 128.15: 9029 128.15 - 135.67: 341 Bond angle restraints: 34866 Sorted by residual: angle pdb=" N ARG L 39 " pdb=" CA ARG L 39 " pdb=" C ARG L 39 " ideal model delta sigma weight residual 111.14 123.18 -12.04 1.08e+00 8.57e-01 1.24e+02 angle pdb=" N PRO L 17 " pdb=" CA PRO L 17 " pdb=" C PRO L 17 " ideal model delta sigma weight residual 112.47 129.35 -16.88 2.06e+00 2.36e-01 6.71e+01 angle pdb=" N TRP C 168 " pdb=" CA TRP C 168 " pdb=" C TRP C 168 " ideal model delta sigma weight residual 111.14 118.89 -7.75 1.08e+00 8.57e-01 5.15e+01 angle pdb=" C PRO L 13 " pdb=" N GLU L 14 " pdb=" CA GLU L 14 " ideal model delta sigma weight residual 120.28 129.18 -8.90 1.34e+00 5.57e-01 4.41e+01 angle pdb=" C GLN L 19 " pdb=" N LEU L 20 " pdb=" CA LEU L 20 " ideal model delta sigma weight residual 120.38 128.89 -8.51 1.37e+00 5.33e-01 3.86e+01 ... (remaining 34861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 14207 35.45 - 70.89: 803 70.89 - 106.34: 64 106.34 - 141.78: 3 141.78 - 177.23: 7 Dihedral angle restraints: 15084 sinusoidal: 6599 harmonic: 8485 Sorted by residual: dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual 232.00 54.77 177.23 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 39 " pdb=" C1' U M 39 " pdb=" N1 U M 39 " pdb=" C2 U M 39 " ideal model delta sinusoidal sigma weight residual -128.00 48.54 -176.54 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 37 " pdb=" C1' C M 37 " pdb=" N1 C M 37 " pdb=" C2 C M 37 " ideal model delta sinusoidal sigma weight residual 232.00 61.19 170.81 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 15081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3482 0.073 - 0.147: 448 0.147 - 0.220: 38 0.220 - 0.293: 5 0.293 - 0.366: 2 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA PRO L 17 " pdb=" N PRO L 17 " pdb=" C PRO L 17 " pdb=" CB PRO L 17 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA GLN A 225 " pdb=" N GLN A 225 " pdb=" C GLN A 225 " pdb=" CB GLN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3972 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU L 14 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLU L 14 " -0.079 2.00e-02 2.50e+03 pdb=" O GLU L 14 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE L 15 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 169 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ARG C 169 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG C 169 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN C 170 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 103 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 104 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO F 104 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 104 " -0.044 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 668 2.68 - 3.24: 20904 3.24 - 3.79: 39219 3.79 - 4.35: 50429 4.35 - 4.90: 83111 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O PRO L 17 " pdb=" N GLN L 19 " model vdw 2.129 2.520 nonbonded pdb=" O GLN L 19 " pdb=" OG SER L 22 " model vdw 2.219 2.440 nonbonded pdb=" O2' C M 50 " pdb=" OP1 U M 52 " model vdw 2.239 2.440 nonbonded pdb=" N ASP L 38 " pdb=" OD1 ASP L 38 " model vdw 2.261 2.520 nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.279 2.440 ... (remaining 194326 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 'C' and (resid 25 through 51 or (resid 52 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 165 or (resid 166 throu \ gh 171 and (name N or name CA or name C or name O or name CB )) or resid 172 thr \ ough 291 or (resid 292 through 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 319 or (resid 320 through 321 and (name N or na \ me CA or name C or name O or name CB )) or resid 322 through 334 or (resid 335 t \ hrough 336 and (name N or name CA or name C or name O or name CB )) or resid 337 \ through 357)) selection = (chain 'D' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 250 or resid 263 through 317 or (resid 318 and (name N or name C \ A or name C or name O or name CB )) or resid 319 through 334 or (resid 335 throu \ gh 336 and (name N or name CA or name C or name O or name CB )) or resid 337 thr \ ough 357)) selection = (chain 'F' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) \ or resid 297 through 317 or (resid 318 and (name N or name CA or name C or name \ O or name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or \ name C or name O or name CB )) or resid 322 through 334 or (resid 335 through 3 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 337 through \ 357)) selection = (chain 'G' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 250 or resid 263 through 290 or (resid 291 through 294 and (name \ N or name CA or name C or name O or name CB )) or resid 295 through 317 or (res \ id 318 and (name N or name CA or name C or name O or name CB )) or resid 319 or \ (resid 320 through 321 and (name N or name CA or name C or name O or name CB )) \ or resid 322 through 334 or (resid 335 through 336 and (name N or name CA or nam \ e C or name O or name CB )) or resid 337 through 357)) selection = (chain 'H' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 166 or (resid 167 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 295 or (res \ id 296 and (name N or name CA or name C or name O or name CB )) or resid 297 thr \ ough 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) \ or resid 319 or (resid 320 through 321 and (name N or name CA or name C or name \ O or name CB )) or resid 322 through 334 or (resid 335 through 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 through 357)) selection = (chain 'I' and (resid 25 through 48 or (resid 49 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 67 or resid 96 through \ 165 or (resid 166 through 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 250 or resid 263 through 291 or (res \ id 292 through 294 and (name N or name CA or name C or name O or name CB )) or r \ esid 295 through 317 or (resid 318 and (name N or name CA or name C or name O or \ name CB )) or resid 319 or (resid 320 through 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 357)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.900 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: 4.290 Check model and map are aligned: 0.360 Set scattering table: 0.180 Process input model: 67.960 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.090 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 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 : 0.005 0.057 25296 Z= 0.326 Angle : 0.908 16.880 34866 Z= 0.517 Chirality : 0.050 0.366 3975 Planarity : 0.007 0.081 4196 Dihedral : 20.462 177.230 9602 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.96 % Favored : 91.97 % Rotamer: Outliers : 7.08 % Allowed : 17.46 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.12), residues: 2915 helix: -2.92 (0.12), residues: 837 sheet: -0.84 (0.24), residues: 432 loop : -3.51 (0.11), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 228 HIS 0.006 0.001 HIS G 343 PHE 0.019 0.002 PHE C 235 TYR 0.021 0.002 TYR G 290 ARG 0.011 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 322 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7240 (tp) REVERT: A 156 ARG cc_start: 0.6210 (tmt170) cc_final: 0.5109 (tpt170) REVERT: A 193 LEU cc_start: 0.7991 (mt) cc_final: 0.7781 (mt) REVERT: A 390 ARG cc_start: 0.6708 (ttm170) cc_final: 0.6479 (ttm110) REVERT: C 117 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6287 (ptt180) REVERT: C 283 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6310 (mp) REVERT: C 333 ARG cc_start: 0.2880 (OUTLIER) cc_final: 0.2627 (mtm180) REVERT: D 198 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1957 (mt) REVERT: E 124 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6623 (pp30) REVERT: E 133 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7362 (tm-30) REVERT: E 138 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7085 (mtt90) REVERT: F 113 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6887 (ttt90) REVERT: G 31 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6614 (tt) REVERT: G 91 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5570 (mt0) REVERT: H 117 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: H 138 LEU cc_start: 0.8000 (mt) cc_final: 0.7774 (mp) REVERT: H 285 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7581 (m) REVERT: L 24 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6494 (tp) REVERT: L 40 ILE cc_start: 0.6289 (OUTLIER) cc_final: 0.5967 (pt) REVERT: L 102 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5079 (ppt90) outliers start: 154 outliers final: 93 residues processed: 447 average time/residue: 0.4035 time to fit residues: 269.0579 Evaluate side-chains 408 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 300 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 113 ARG Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 325 THR Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 17 PRO Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 38 ASP Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 102 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 77 optimal weight: 0.0050 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 241 GLN A 283 HIS ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 183 HIS C 186 GLN C 275 HIS C 341 GLN C 348 ASN D 160 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN E 82 ASN E 129 GLN E 168 GLN E 194 GLN E 195 GLN E 293 HIS F 91 GLN F 102 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN F 242 GLN F 281 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN G 56 GLN G 94 ASN ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN H 163 ASN H 242 GLN H 329 ASN I 91 GLN I 102 ASN J 27 GLN L 61 HIS L 104 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25296 Z= 0.206 Angle : 0.585 13.403 34866 Z= 0.309 Chirality : 0.040 0.211 3975 Planarity : 0.005 0.057 4196 Dihedral : 19.717 176.599 4889 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer: Outliers : 5.10 % Allowed : 21.78 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.13), residues: 2915 helix: -1.03 (0.16), residues: 839 sheet: -0.56 (0.24), residues: 455 loop : -3.09 (0.12), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 193 HIS 0.010 0.001 HIS E 114 PHE 0.020 0.002 PHE C 323 TYR 0.017 0.002 TYR G 290 ARG 0.007 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 304 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6306 (tt) REVERT: A 63 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7014 (tp) REVERT: A 65 LEU cc_start: 0.6381 (mm) cc_final: 0.6172 (mm) REVERT: A 105 VAL cc_start: 0.6177 (OUTLIER) cc_final: 0.5602 (t) REVERT: A 156 ARG cc_start: 0.6276 (tmt170) cc_final: 0.5094 (tpt170) REVERT: A 235 TYR cc_start: 0.6961 (m-80) cc_final: 0.6509 (m-80) REVERT: A 390 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6550 (mtp-110) REVERT: C 186 GLN cc_start: 0.4970 (OUTLIER) cc_final: 0.4640 (pm20) REVERT: E 133 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7444 (tm-30) REVERT: E 138 ARG cc_start: 0.7299 (ptp-170) cc_final: 0.6799 (mtt90) REVERT: F 113 ARG cc_start: 0.7122 (ttt90) cc_final: 0.6765 (ttt90) REVERT: G 31 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6610 (tt) REVERT: H 117 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: H 302 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6361 (mm-30) REVERT: L 24 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6607 (tp) REVERT: L 83 LEU cc_start: 0.6039 (mt) cc_final: 0.5790 (mt) REVERT: L 118 ARG cc_start: 0.6905 (tpm170) cc_final: 0.6629 (tpm170) outliers start: 111 outliers final: 66 residues processed: 392 average time/residue: 0.4085 time to fit residues: 238.5535 Evaluate side-chains 372 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 299 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 293 optimal weight: 7.9990 chunk 242 optimal weight: 0.0980 chunk 269 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 305 GLN C 275 HIS ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 GLN ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 ASN L 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25296 Z= 0.228 Angle : 0.586 12.227 34866 Z= 0.307 Chirality : 0.040 0.222 3975 Planarity : 0.004 0.050 4196 Dihedral : 19.519 176.550 4781 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 6.39 % Allowed : 21.88 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 2915 helix: -0.23 (0.17), residues: 850 sheet: -0.28 (0.25), residues: 448 loop : -2.89 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 330 HIS 0.010 0.001 HIS E 114 PHE 0.015 0.002 PHE G 114 TYR 0.023 0.002 TYR D 266 ARG 0.008 0.000 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 314 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6369 (tt) REVERT: A 63 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6975 (tp) REVERT: A 65 LEU cc_start: 0.6499 (mm) cc_final: 0.6216 (mm) REVERT: A 105 VAL cc_start: 0.6222 (OUTLIER) cc_final: 0.5616 (t) REVERT: A 156 ARG cc_start: 0.6278 (tmt170) cc_final: 0.5081 (tpt170) REVERT: A 235 TYR cc_start: 0.6957 (m-80) cc_final: 0.6514 (m-80) REVERT: D 108 ASP cc_start: 0.6121 (p0) cc_final: 0.5777 (p0) REVERT: E 107 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.6965 (p) REVERT: E 138 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.6862 (mtt90) REVERT: F 113 ARG cc_start: 0.7207 (ttt90) cc_final: 0.6854 (ttt90) REVERT: F 208 ASP cc_start: 0.6401 (t0) cc_final: 0.6175 (t0) REVERT: G 31 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6595 (tt) REVERT: G 229 LEU cc_start: 0.7477 (tp) cc_final: 0.7188 (tp) REVERT: H 302 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6313 (mm-30) REVERT: L 24 LEU cc_start: 0.6966 (tp) cc_final: 0.6732 (tp) REVERT: L 83 LEU cc_start: 0.6042 (mt) cc_final: 0.5814 (mt) REVERT: L 118 ARG cc_start: 0.6882 (tpm170) cc_final: 0.6660 (tpm170) outliers start: 139 outliers final: 96 residues processed: 415 average time/residue: 0.3977 time to fit residues: 247.5253 Evaluate side-chains 404 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 303 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 290 TYR Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.4980 chunk 204 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 305 GLN A 324 GLN C 170 ASN C 186 GLN C 275 HIS D 148 GLN ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 129 ASN G 343 HIS H 186 GLN I 102 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25296 Z= 0.315 Angle : 0.635 12.356 34866 Z= 0.334 Chirality : 0.042 0.246 3975 Planarity : 0.005 0.058 4196 Dihedral : 19.590 176.651 4779 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 7.08 % Allowed : 22.52 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 2915 helix: -0.12 (0.17), residues: 850 sheet: -0.09 (0.25), residues: 448 loop : -2.85 (0.13), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 49 HIS 0.010 0.001 HIS E 114 PHE 0.029 0.002 PHE D 245 TYR 0.022 0.002 TYR I 144 ARG 0.009 0.000 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 311 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6412 (tt) REVERT: A 63 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6912 (tp) REVERT: A 65 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6210 (mm) REVERT: A 105 VAL cc_start: 0.6233 (OUTLIER) cc_final: 0.5634 (t) REVERT: A 156 ARG cc_start: 0.6316 (tmt170) cc_final: 0.5102 (tpt170) REVERT: A 235 TYR cc_start: 0.6983 (m-80) cc_final: 0.6600 (m-80) REVERT: A 390 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6574 (mtp-110) REVERT: E 107 VAL cc_start: 0.7372 (OUTLIER) cc_final: 0.7091 (p) REVERT: E 138 ARG cc_start: 0.7359 (ptp-170) cc_final: 0.7011 (mtt90) REVERT: F 113 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6935 (ttt90) REVERT: F 169 ARG cc_start: 0.5939 (ttt180) cc_final: 0.5692 (ttt180) REVERT: F 186 GLN cc_start: 0.4648 (OUTLIER) cc_final: 0.4057 (mt0) REVERT: G 31 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6703 (tt) REVERT: G 113 ARG cc_start: 0.7086 (ttt-90) cc_final: 0.6627 (ttt-90) REVERT: G 231 GLU cc_start: 0.7492 (tt0) cc_final: 0.6849 (tt0) REVERT: H 302 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6282 (mm-30) REVERT: I 249 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: I 290 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6408 (p90) REVERT: L 24 LEU cc_start: 0.7132 (tp) cc_final: 0.6919 (tp) REVERT: L 83 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5867 (mt) outliers start: 154 outliers final: 119 residues processed: 427 average time/residue: 0.4017 time to fit residues: 257.6560 Evaluate side-chains 432 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 303 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 147 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 389 ASN C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN I 102 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25296 Z= 0.309 Angle : 0.630 12.360 34866 Z= 0.331 Chirality : 0.042 0.243 3975 Planarity : 0.005 0.055 4196 Dihedral : 19.534 176.501 4779 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.57 % Favored : 90.39 % Rotamer: Outliers : 7.22 % Allowed : 23.30 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2915 helix: 0.02 (0.17), residues: 850 sheet: -0.07 (0.25), residues: 456 loop : -2.83 (0.13), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 49 HIS 0.009 0.001 HIS E 114 PHE 0.027 0.002 PHE D 245 TYR 0.020 0.002 TYR I 144 ARG 0.007 0.000 ARG F 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 303 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6400 (tt) REVERT: A 63 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6723 (tp) REVERT: A 65 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6227 (mm) REVERT: A 105 VAL cc_start: 0.6186 (OUTLIER) cc_final: 0.5595 (t) REVERT: A 156 ARG cc_start: 0.6327 (tmt170) cc_final: 0.5098 (tpt170) REVERT: A 235 TYR cc_start: 0.6969 (m-80) cc_final: 0.6583 (m-80) REVERT: A 390 ARG cc_start: 0.6826 (ttm170) cc_final: 0.6559 (mtp-110) REVERT: E 107 VAL cc_start: 0.7376 (OUTLIER) cc_final: 0.7093 (p) REVERT: E 116 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5790 (p0) REVERT: E 138 ARG cc_start: 0.7399 (ptp-170) cc_final: 0.7065 (mtt90) REVERT: F 113 ARG cc_start: 0.7200 (ttt90) cc_final: 0.6982 (ttt90) REVERT: F 186 GLN cc_start: 0.4636 (OUTLIER) cc_final: 0.4049 (mt0) REVERT: G 31 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6704 (tt) REVERT: G 113 ARG cc_start: 0.7053 (ttt-90) cc_final: 0.6533 (ttt-90) REVERT: G 231 GLU cc_start: 0.7500 (tt0) cc_final: 0.6711 (tt0) REVERT: H 302 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6291 (mm-30) REVERT: I 249 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: I 290 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6406 (p90) REVERT: L 24 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6822 (tp) REVERT: L 83 LEU cc_start: 0.6152 (mt) cc_final: 0.5897 (mt) REVERT: L 118 ARG cc_start: 0.6583 (tpm170) cc_final: 0.5944 (tpm170) outliers start: 157 outliers final: 125 residues processed: 422 average time/residue: 0.3975 time to fit residues: 252.0171 Evaluate side-chains 435 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 299 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 249 GLU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 290 TYR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 143 THR Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 159 HIS Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 2.9990 chunk 260 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 169 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 289 optimal weight: 0.0770 chunk 240 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25296 Z= 0.159 Angle : 0.552 11.558 34866 Z= 0.289 Chirality : 0.039 0.227 3975 Planarity : 0.004 0.055 4196 Dihedral : 19.282 176.955 4775 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 5.51 % Allowed : 25.37 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 2915 helix: 0.60 (0.18), residues: 858 sheet: 0.15 (0.25), residues: 435 loop : -2.66 (0.13), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 193 HIS 0.010 0.001 HIS E 114 PHE 0.009 0.001 PHE F 166 TYR 0.022 0.001 TYR I 144 ARG 0.007 0.000 ARG D 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 294 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7186 (mp) cc_final: 0.6720 (tp) REVERT: A 65 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6166 (mm) REVERT: A 156 ARG cc_start: 0.6278 (tmt170) cc_final: 0.5070 (tpt170) REVERT: A 226 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6557 (mt-10) REVERT: A 235 TYR cc_start: 0.6897 (m-80) cc_final: 0.6430 (m-80) REVERT: A 339 ARG cc_start: 0.5940 (ttm110) cc_final: 0.5619 (ttm110) REVERT: E 138 ARG cc_start: 0.7336 (ptp-170) cc_final: 0.6847 (mtt90) REVERT: F 113 ARG cc_start: 0.7120 (ttt90) cc_final: 0.6825 (ttt90) REVERT: F 169 ARG cc_start: 0.5852 (ttt180) cc_final: 0.5604 (ttt180) REVERT: F 186 GLN cc_start: 0.4592 (OUTLIER) cc_final: 0.4001 (mt0) REVERT: G 31 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6603 (tt) REVERT: G 64 ARG cc_start: 0.6383 (ptt90) cc_final: 0.6128 (ptt90) REVERT: H 43 LEU cc_start: 0.7392 (mm) cc_final: 0.7130 (mt) REVERT: H 110 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7523 (tp) REVERT: H 302 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6306 (mm-30) REVERT: I 249 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: I 290 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6360 (p90) REVERT: L 1 MET cc_start: 0.1901 (mmm) cc_final: 0.1122 (mmm) REVERT: L 24 LEU cc_start: 0.7051 (tp) cc_final: 0.6772 (tp) REVERT: L 83 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5997 (mt) REVERT: L 118 ARG cc_start: 0.6313 (tpm170) cc_final: 0.5638 (tpm170) outliers start: 120 outliers final: 91 residues processed: 384 average time/residue: 0.4109 time to fit residues: 234.8068 Evaluate side-chains 393 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 294 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 186 GLN Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ARG Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 chunk 180 optimal weight: 0.0870 chunk 175 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25296 Z= 0.229 Angle : 0.583 11.190 34866 Z= 0.304 Chirality : 0.040 0.233 3975 Planarity : 0.004 0.052 4196 Dihedral : 19.262 177.104 4765 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.75 % Favored : 91.22 % Rotamer: Outliers : 5.70 % Allowed : 25.28 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 2915 helix: 0.68 (0.18), residues: 853 sheet: 0.24 (0.25), residues: 435 loop : -2.62 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 330 HIS 0.010 0.001 HIS E 114 PHE 0.019 0.002 PHE D 245 TYR 0.022 0.002 TYR I 144 ARG 0.013 0.000 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 295 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6189 (mm) REVERT: A 156 ARG cc_start: 0.6321 (tmt170) cc_final: 0.5090 (tpt170) REVERT: A 226 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6764 (mt-10) REVERT: A 235 TYR cc_start: 0.6922 (m-80) cc_final: 0.6485 (m-80) REVERT: A 339 ARG cc_start: 0.6034 (ttm110) cc_final: 0.5709 (ttm110) REVERT: C 333 ARG cc_start: 0.3058 (OUTLIER) cc_final: 0.2703 (mtm180) REVERT: E 138 ARG cc_start: 0.7382 (ptp-170) cc_final: 0.7021 (mtt90) REVERT: E 193 LEU cc_start: 0.8125 (mt) cc_final: 0.7846 (tp) REVERT: F 35 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6003 (ptp90) REVERT: G 31 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6584 (tt) REVERT: H 110 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7638 (tp) REVERT: H 302 GLU cc_start: 0.6553 (mm-30) cc_final: 0.6307 (mm-30) REVERT: I 249 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: I 290 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6489 (p90) REVERT: L 1 MET cc_start: 0.2514 (OUTLIER) cc_final: 0.1877 (mmm) REVERT: L 24 LEU cc_start: 0.7134 (tp) cc_final: 0.6848 (tp) REVERT: L 83 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6052 (mt) REVERT: L 118 ARG cc_start: 0.6409 (tpm170) cc_final: 0.5751 (tpm170) outliers start: 124 outliers final: 101 residues processed: 393 average time/residue: 0.4074 time to fit residues: 238.7331 Evaluate side-chains 403 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 292 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25296 Z= 0.204 Angle : 0.575 11.132 34866 Z= 0.300 Chirality : 0.040 0.245 3975 Planarity : 0.004 0.056 4196 Dihedral : 19.216 177.146 4763 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.51 % Favored : 91.46 % Rotamer: Outliers : 5.84 % Allowed : 24.77 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2915 helix: 0.78 (0.18), residues: 851 sheet: 0.29 (0.26), residues: 426 loop : -2.56 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 193 HIS 0.011 0.001 HIS E 114 PHE 0.016 0.001 PHE D 245 TYR 0.023 0.002 TYR I 144 ARG 0.013 0.000 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 296 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6169 (mm) REVERT: A 235 TYR cc_start: 0.6930 (m-80) cc_final: 0.6476 (m-80) REVERT: A 305 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6777 (mp10) REVERT: C 333 ARG cc_start: 0.3117 (OUTLIER) cc_final: 0.2753 (mtm180) REVERT: E 116 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5677 (p0) REVERT: E 138 ARG cc_start: 0.7347 (ptp-170) cc_final: 0.7008 (mtt90) REVERT: E 167 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3960 (pm20) REVERT: F 35 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5996 (ptp90) REVERT: G 31 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6577 (tt) REVERT: H 110 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7632 (tp) REVERT: H 302 GLU cc_start: 0.6548 (mm-30) cc_final: 0.6280 (mm-30) REVERT: I 249 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: I 290 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6449 (p90) REVERT: L 1 MET cc_start: 0.2403 (OUTLIER) cc_final: 0.1871 (mmm) REVERT: L 24 LEU cc_start: 0.7130 (tp) cc_final: 0.6817 (tp) REVERT: L 83 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.6033 (mt) outliers start: 127 outliers final: 108 residues processed: 393 average time/residue: 0.4163 time to fit residues: 243.6250 Evaluate side-chains 412 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 292 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 227 HIS Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 0.6980 chunk 276 optimal weight: 3.9990 chunk 251 optimal weight: 0.9980 chunk 268 optimal weight: 0.8980 chunk 161 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 267 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25296 Z= 0.170 Angle : 0.559 10.781 34866 Z= 0.291 Chirality : 0.039 0.257 3975 Planarity : 0.004 0.064 4196 Dihedral : 19.128 177.266 4762 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.13 % Favored : 91.84 % Rotamer: Outliers : 5.93 % Allowed : 24.68 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2915 helix: 0.94 (0.18), residues: 852 sheet: 0.33 (0.26), residues: 431 loop : -2.52 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 26 HIS 0.011 0.001 HIS E 114 PHE 0.011 0.001 PHE D 245 TYR 0.024 0.001 TYR I 144 ARG 0.014 0.000 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 295 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6163 (mm) REVERT: A 108 VAL cc_start: 0.5495 (OUTLIER) cc_final: 0.5270 (t) REVERT: A 226 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: A 235 TYR cc_start: 0.6889 (m-80) cc_final: 0.6433 (m-80) REVERT: A 305 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6777 (mp10) REVERT: C 333 ARG cc_start: 0.3186 (OUTLIER) cc_final: 0.2688 (mtm180) REVERT: E 116 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5613 (p0) REVERT: E 138 ARG cc_start: 0.7334 (ptp-170) cc_final: 0.6972 (mtt90) REVERT: E 167 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.4007 (pm20) REVERT: F 35 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5898 (ptp90) REVERT: F 168 TRP cc_start: 0.7125 (m100) cc_final: 0.6314 (m100) REVERT: G 31 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6618 (tt) REVERT: H 277 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: H 302 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6259 (mm-30) REVERT: I 249 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: I 290 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6390 (p90) REVERT: L 1 MET cc_start: 0.2163 (mmm) cc_final: 0.1759 (mmm) REVERT: L 25 PHE cc_start: 0.5770 (t80) cc_final: 0.5531 (t80) REVERT: L 83 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5989 (mt) outliers start: 129 outliers final: 106 residues processed: 396 average time/residue: 0.4302 time to fit residues: 253.5722 Evaluate side-chains 411 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 292 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 297 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 237 optimal weight: 0.0000 chunk 24 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25296 Z= 0.187 Angle : 0.567 11.146 34866 Z= 0.295 Chirality : 0.039 0.264 3975 Planarity : 0.004 0.063 4196 Dihedral : 19.077 177.159 4755 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.27 % Favored : 91.70 % Rotamer: Outliers : 5.74 % Allowed : 25.18 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 2915 helix: 0.97 (0.18), residues: 857 sheet: 0.37 (0.26), residues: 429 loop : -2.50 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 26 HIS 0.011 0.001 HIS E 114 PHE 0.023 0.001 PHE L 44 TYR 0.023 0.002 TYR I 144 ARG 0.015 0.000 ARG H 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5830 Ramachandran restraints generated. 2915 Oldfield, 0 Emsley, 2915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 291 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6184 (mm) REVERT: A 226 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6663 (mt-10) REVERT: A 235 TYR cc_start: 0.6904 (m-80) cc_final: 0.6447 (m-80) REVERT: A 305 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: C 333 ARG cc_start: 0.3146 (OUTLIER) cc_final: 0.2668 (mtm180) REVERT: E 116 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5604 (p0) REVERT: E 138 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.6937 (mtt90) REVERT: E 167 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.3971 (pm20) REVERT: F 35 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5935 (ptp90) REVERT: F 113 ARG cc_start: 0.7036 (ttt90) cc_final: 0.6713 (ttt90) REVERT: F 168 TRP cc_start: 0.7136 (m100) cc_final: 0.6326 (m100) REVERT: G 31 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6603 (tt) REVERT: H 34 GLU cc_start: 0.6536 (tp30) cc_final: 0.6251 (tp30) REVERT: H 277 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6934 (pt0) REVERT: H 302 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6281 (mm-30) REVERT: I 249 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: I 290 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6377 (p90) REVERT: L 1 MET cc_start: 0.2121 (mmm) cc_final: 0.1797 (mmm) REVERT: L 25 PHE cc_start: 0.5765 (t80) cc_final: 0.5559 (t80) REVERT: L 83 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5982 (mt) outliers start: 125 outliers final: 109 residues processed: 385 average time/residue: 0.4079 time to fit residues: 233.6867 Evaluate side-chains 409 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 288 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 305 GLN Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 227 HIS Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 290 TYR Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 128 CYS Chi-restraints excluded: chain G residue 146 ASN Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 316 GLN Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 233 VAL Chi-restraints excluded: chain H residue 240 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 289 TRP Chi-restraints excluded: chain H residue 320 LYS Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 102 ASN Chi-restraints excluded: chain I residue 128 CYS Chi-restraints excluded: chain I residue 200 ILE Chi-restraints excluded: chain I residue 231 GLU Chi-restraints excluded: chain I residue 249 GLU Chi-restraints excluded: chain I residue 289 TRP Chi-restraints excluded: chain I residue 290 TYR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 355 PHE Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 54 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 39 ARG Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 119 ARG Chi-restraints excluded: chain L residue 144 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 0.0670 chunk 99 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.166061 restraints weight = 35921.607| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.54 r_work: 0.3871 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 25296 Z= 0.226 Angle : 0.713 59.189 34866 Z= 0.400 Chirality : 0.041 0.678 3975 Planarity : 0.005 0.102 4196 Dihedral : 19.086 177.156 4752 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.63 % Rotamer: Outliers : 5.74 % Allowed : 25.37 % Favored : 68.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.38 (0.15), residues: 2915 helix: 0.98 (0.18), residues: 857 sheet: 0.36 (0.26), residues: 429 loop : -2.49 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 26 HIS 0.010 0.001 HIS E 114 PHE 0.020 0.001 PHE L 44 TYR 0.021 0.002 TYR I 144 ARG 0.013 0.000 ARG H 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5498.90 seconds wall clock time: 99 minutes 8.32 seconds (5948.32 seconds total)