Starting phenix.real_space_refine on Tue Mar 19 12:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecv_31058/03_2024/7ecv_31058.pdb" } resolution = 3.43 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= 0.001 sd= 0.013 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 59 5.49 5 S 33 5.16 5 C 14826 2.51 5 N 4458 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 49": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L GLU 124": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 169": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 169": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 166": "NH1" <-> "NH2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "H GLU 15": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "I GLU 5": "OE1" <-> "OE2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J GLU 8": "OE1" <-> "OE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24153 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1423 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 185, 1420 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 59 Conformer: "B" Number of residues, atoms: 185, 1420 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 59 bond proxies already assigned to first conformer: 1452 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2065 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 309, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1402 Unresolved non-hydrogen angles: 2023 Unresolved non-hydrogen dihedrals: 916 Unresolved non-hydrogen chiralities: 389 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 9, 'HIS:plan': 11, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 756 Chain: "B" Number of atoms: 2368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2368 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2265 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2548 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2560 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2574 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2560 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2547 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 318} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1272 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 22, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 13.47, per 1000 atoms: 0.56 Number of scatterers: 24153 At special positions: 0 Unit cell: (154, 144.1, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 59 15.00 O 4777 8.00 N 4458 7.00 C 14826 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: 9.15 Conformation dependent library (CDL) restraints added in 4.5 seconds 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5196 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 42 sheets defined 31.7% alpha, 17.1% beta 0 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.63 Creating SS restraints... Processing helix chain 'L' and resid 16 through 36 Processing helix chain 'L' and resid 63 through 72 removed outlier: 3.933A pdb=" N ALA L 72 " --> pdb=" O ARG L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.601A pdb=" N LEU L 76 " --> pdb=" O ARG L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 121 removed outlier: 3.920A pdb=" N LEU L 112 " --> pdb=" O ASN L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 131 Processing helix chain 'L' and resid 132 through 136 removed outlier: 3.816A pdb=" N VAL L 135 " --> pdb=" O PRO L 132 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA L 136 " --> pdb=" O ASP L 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 132 through 136' Processing helix chain 'A' and resid 16 through 28 removed outlier: 4.422A pdb=" N PHE A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 51 through 63 removed outlier: 3.759A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 294 through 307 removed outlier: 4.091A pdb=" N LEU A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 5.754A pdb=" N ARG A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.621A pdb=" N VAL A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.512A pdb=" N LEU A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP A 362 " --> pdb=" O GLU A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 362' Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.311A pdb=" N ARG A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.665A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 4.130A pdb=" N ALA A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.799A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.810A pdb=" N ALA B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.562A pdb=" N LEU B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.892A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 4.079A pdb=" N LEU B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.974A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.840A pdb=" N ARG C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.697A pdb=" N ASP C 309 " --> pdb=" O TYR C 305 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.594A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 removed outlier: 3.979A pdb=" N ILE D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 129 removed outlier: 3.720A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.909A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 322 through 329 removed outlier: 4.136A pdb=" N VAL D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 removed outlier: 3.944A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.523A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 191 through 204 removed outlier: 3.952A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 removed outlier: 3.834A pdb=" N ALA E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.884A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 4.143A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.689A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 removed outlier: 3.766A pdb=" N ASP G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.649A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 191 through 204 removed outlier: 3.990A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 removed outlier: 3.523A pdb=" N ALA G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.423A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.791A pdb=" N HIS G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 72 removed outlier: 3.693A pdb=" N ASP H 68 " --> pdb=" O PRO H 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.753A pdb=" N ASN H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 204 Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 304 through 313 Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.200A pdb=" N ARG I 13 " --> pdb=" O ILE I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 removed outlier: 3.927A pdb=" N ALA I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 56 removed outlier: 3.511A pdb=" N ALA I 56 " --> pdb=" O GLU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 removed outlier: 3.643A pdb=" N ALA I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 121 removed outlier: 3.644A pdb=" N LEU I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.851A pdb=" N ARG J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 32 removed outlier: 4.234A pdb=" N ALA J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 56 Processing helix chain 'J' and resid 60 through 74 removed outlier: 3.800A pdb=" N ALA J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 121 removed outlier: 3.562A pdb=" N LEU J 113 " --> pdb=" O GLY J 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'L' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'L' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 172 through 173 removed outlier: 4.171A pdb=" N GLY L 172 " --> pdb=" O LYS L 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 178 through 181 Processing sheet with id=AA7, first strand: chain 'A' and resid 178 through 181 removed outlier: 7.360A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 234 removed outlier: 4.468A pdb=" N PHE A 232 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 219 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 234 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS B 217 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 240 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 263 through 264 removed outlier: 4.320A pdb=" N PHE B 81 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 113 removed outlier: 3.738A pdb=" N ALA B 8 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 159 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.664A pdb=" N ARG B 65 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.806A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.567A pdb=" N VAL C 99 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.721A pdb=" N ALA C 23 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 255 " --> pdb=" O ALA C 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 229 through 230 removed outlier: 4.544A pdb=" N THR C 245 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.584A pdb=" N GLY D 334 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.655A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.655A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'D' and resid 44 through 51 Processing sheet with id=AC3, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.738A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 177 removed outlier: 4.006A pdb=" N ARG E 172 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 44 through 49 removed outlier: 4.559A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC8, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.562A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.556A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 19 removed outlier: 4.096A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AD3, first strand: chain 'F' and resid 45 through 46 Processing sheet with id=AD4, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.727A pdb=" N PHE I 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR I 102 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER I 96 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N PHE I 104 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS I 94 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 287 through 288 removed outlier: 3.524A pdb=" N VAL F 288 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 293 " --> pdb=" O VAL F 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 108 through 109 removed outlier: 3.565A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.097A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AD9, first strand: chain 'G' and resid 44 through 51 removed outlier: 7.076A pdb=" N LYS G 242 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR G 78 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS G 244 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.749A pdb=" N VAL G 288 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AE3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.505A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 44 through 51 removed outlier: 4.200A pdb=" N ALA H 82 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 44 through 51 removed outlier: 8.178A pdb=" N THR H 78 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.811A pdb=" N CYS J 106 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 15.211A pdb=" N ASP H 80 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE J 92 " --> pdb=" O TYR J 105 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2622 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6173 1.33 - 1.45: 5105 1.45 - 1.57: 13283 1.57 - 1.69: 118 1.69 - 1.81: 50 Bond restraints: 24729 Sorted by residual: bond pdb=" CA ASN E 75 " pdb=" C ASN E 75 " ideal model delta sigma weight residual 1.526 1.492 0.034 1.08e-02 8.57e+03 9.72e+00 bond pdb=" C TYR F 271 " pdb=" N PRO F 272 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.38e-02 5.25e+03 8.44e+00 bond pdb=" N ASN H 75 " pdb=" CA ASN H 75 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.58e+00 bond pdb=" CG1 ILE E 260 " pdb=" CD1 ILE E 260 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.13e+00 bond pdb=" C TYR B 262 " pdb=" N LEU B 263 " ideal model delta sigma weight residual 1.329 1.262 0.067 3.03e-02 1.09e+03 4.91e+00 ... (remaining 24724 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.56: 965 106.56 - 113.45: 13028 113.45 - 120.35: 9309 120.35 - 127.24: 10013 127.24 - 134.14: 376 Bond angle restraints: 33691 Sorted by residual: angle pdb=" N LEU B 139 " pdb=" CA LEU B 139 " pdb=" C LEU B 139 " ideal model delta sigma weight residual 113.38 122.15 -8.77 1.23e+00 6.61e-01 5.08e+01 angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 112.83 118.95 -6.12 9.90e-01 1.02e+00 3.82e+01 angle pdb=" C ILE D 267 " pdb=" N ASP D 268 " pdb=" CA ASP D 268 " ideal model delta sigma weight residual 123.05 115.48 7.57 1.40e+00 5.10e-01 2.92e+01 angle pdb=" C GLN E 241 " pdb=" CA GLN E 241 " pdb=" CB GLN E 241 " ideal model delta sigma weight residual 116.54 111.04 5.50 1.15e+00 7.56e-01 2.28e+01 angle pdb=" N VAL E 249 " pdb=" CA VAL E 249 " pdb=" C VAL E 249 " ideal model delta sigma weight residual 109.34 100.85 8.49 2.08e+00 2.31e-01 1.67e+01 ... (remaining 33686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 13809 32.37 - 64.74: 605 64.74 - 97.11: 74 97.11 - 129.49: 1 129.49 - 161.86: 4 Dihedral angle restraints: 14493 sinusoidal: 6113 harmonic: 8380 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 47.63 152.37 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 56.99 143.01 1 1.50e+01 4.44e-03 7.67e+01 dihedral pdb=" O4' U M 35 " pdb=" C1' U M 35 " pdb=" N1 U M 35 " pdb=" C2 U M 35 " ideal model delta sinusoidal sigma weight residual -160.00 -78.28 -81.72 1 1.50e+01 4.44e-03 3.65e+01 ... (remaining 14490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3011 0.067 - 0.133: 526 0.133 - 0.200: 70 0.200 - 0.266: 9 0.266 - 0.333: 1 Chirality restraints: 3617 Sorted by residual: chirality pdb=" CA LEU B 139 " pdb=" N LEU B 139 " pdb=" C LEU B 139 " pdb=" CB LEU B 139 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB VAL L 42 " pdb=" CA VAL L 42 " pdb=" CG1 VAL L 42 " pdb=" CG2 VAL L 42 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR B 318 " pdb=" CA THR B 318 " pdb=" OG1 THR B 318 " pdb=" CG2 THR B 318 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3614 not shown) Planarity restraints: 4314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR F 271 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO F 272 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 266 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR D 266 " 0.044 2.00e-02 2.50e+03 pdb=" O THR D 266 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE D 267 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG L 73 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO L 74 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO L 74 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 74 " -0.034 5.00e-02 4.00e+02 ... (remaining 4311 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 109 2.43 - 3.05: 13475 3.05 - 3.67: 35975 3.67 - 4.28: 52651 4.28 - 4.90: 89129 Nonbonded interactions: 191339 Sorted by model distance: nonbonded pdb=" NH2 ARG L 102 " pdb=" CZ PHE L 155 " model vdw 1.818 3.420 nonbonded pdb=" CE1 TYR A 179 " pdb=" CD1 LEU A 189 " model vdw 1.821 3.760 nonbonded pdb=" O ASP D 303 " pdb=" CD2 LEU D 307 " model vdw 1.834 3.460 nonbonded pdb=" OD1 ASP D 303 " pdb=" N TYR D 305 " model vdw 1.905 2.520 nonbonded pdb=" OD1 ASP D 303 " pdb=" N PHE D 304 " model vdw 2.028 2.520 ... (remaining 191334 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 6 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 211 or (resid 212 and (name N or na \ me CA or name C or name O or name CB )) or resid 213 through 249 or (resid 250 a \ nd (name N or name CA or name C or name O or name CB )) or resid 251 through 272 \ or (resid 273 through 275 and (name N or name CA or name C or name O or name CB \ )) or resid 276 through 282 or (resid 283 and (name N or name CA or name C or n \ ame O or name CB )) or resid 284 through 336)) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 211 or (resid 212 and (na \ me N or name CA or name C or name O or name CB )) or resid 213 through 231 or re \ sid 244 through 282 or (resid 283 and (name N or name CA or name C or name O or \ name CB )) or resid 284 through 292 or (resid 293 through 294 and (name N or nam \ e CA or name C or name O or name CB )) or resid 295 through 302 or (resid 303 an \ d (name N or name CA or name C or name O or name CB )) or resid 304 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 336)) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 292 or (resid 293 through 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 302 or \ (resid 303 and (name N or name CA or name C or name O or name CB )) or resid 304 \ through 306 or (resid 307 and (name N or name CA or name C or name O or name CB \ )) or resid 308 through 336)) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 282 or (resid 283 and (name N or na \ me CA or name C or name O or name CB )) or resid 284 through 292 or (resid 293 t \ hrough 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ through 302 or (resid 303 and (name N or name CA or name C or name O or name CB \ )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C or n \ ame O or name CB )) or resid 308 through 336)) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or resid 244 through 249 or (resid 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 282 or (resid 283 and (name N or na \ me CA or name C or name O or name CB )) or resid 284 through 292 or (resid 293 t \ hrough 294 and (name N or name CA or name C or name O or name CB )) or resid 295 \ through 302 or (resid 303 and (name N or name CA or name C or name O or name CB \ )) or resid 304 through 306 or (resid 307 and (name N or name CA or name C or n \ ame O or name CB )) or resid 308 through 336)) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 79 or (resid 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 through 231 or resid \ 244 through 249 or (resid 250 and (name N or name CA or name C or name O or nam \ e CB )) or resid 251 through 292 or (resid 293 through 294 and (name N or name C \ A or name C or name O or name CB )) or resid 295 through 302 or (resid 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 306 or \ (resid 307 and (name N or name CA or name C or name O or name CB )) or resid 308 \ through 336)) } ncs_group { reference = (chain 'I' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 50 or (re \ sid 51 and (name N or name CA or name C or name O or name CB )) or resid 52 thro \ ugh 62 or (resid 63 through 64 and (name N or name CA or name C or name O or nam \ e CB )) or resid 65 through 124)) selection = (chain 'J' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.370 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: 3.230 Check model and map are aligned: 0.360 Set scattering table: 0.200 Process input model: 65.280 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.006 0.088 24729 Z= 0.392 Angle : 0.856 9.841 33691 Z= 0.482 Chirality : 0.052 0.333 3617 Planarity : 0.006 0.067 4314 Dihedral : 17.828 161.857 9297 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 0.87 % Allowed : 14.05 % Favored : 85.08 % 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: -4.11 (0.12), residues: 3092 helix: -2.79 (0.12), residues: 940 sheet: -1.72 (0.22), residues: 510 loop : -3.09 (0.12), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 263 HIS 0.011 0.002 HIS L 61 PHE 0.021 0.002 PHE G 95 TYR 0.021 0.002 TYR E 247 ARG 0.011 0.001 ARG L 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 447 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7074 (pt0) cc_final: 0.6855 (pt0) REVERT: B 131 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7149 (tm-30) REVERT: B 258 LEU cc_start: 0.8139 (pt) cc_final: 0.7853 (pp) REVERT: C 140 HIS cc_start: 0.7342 (m-70) cc_final: 0.7037 (t-90) REVERT: C 283 GLU cc_start: 0.7226 (tp30) cc_final: 0.6959 (tp30) REVERT: D 303 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7486 (p0) REVERT: E 302 LEU cc_start: 0.8637 (mt) cc_final: 0.8317 (mp) REVERT: E 322 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: H 89 ASP cc_start: 0.7990 (t70) cc_final: 0.7701 (t0) REVERT: H 244 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8289 (ttpp) REVERT: I 7 ILE cc_start: 0.7076 (mm) cc_final: 0.6701 (mm) REVERT: I 8 GLU cc_start: 0.7456 (pp20) cc_final: 0.6848 (pp20) outliers start: 19 outliers final: 13 residues processed: 461 average time/residue: 0.4322 time to fit residues: 289.4320 Evaluate side-chains 349 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 334 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain G residue 144 ASN Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 246 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 285 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 108 ASN ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 230 HIS B 69 GLN B 82 ASN B 89 ASN B 104 HIS B 114 HIS B 172 ASN B 173 GLN C 77 GLN C 129 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 163 ASN D 164 HIS E 127 ASN E 163 ASN E 208 HIS E 223 GLN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN F 208 HIS G 163 ASN G 310 ASN G 322 GLN H 77 GLN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 208 HIS H 310 ASN H 329 ASN ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 ASN J 55 GLN J 120 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24729 Z= 0.182 Angle : 0.548 10.999 33691 Z= 0.288 Chirality : 0.040 0.203 3617 Planarity : 0.004 0.056 4314 Dihedral : 15.200 177.022 4358 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 3.33 % Allowed : 17.84 % Favored : 78.83 % 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: -2.74 (0.14), residues: 3092 helix: -0.85 (0.16), residues: 961 sheet: -1.35 (0.22), residues: 526 loop : -2.66 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 39 HIS 0.006 0.001 HIS L 161 PHE 0.019 0.001 PHE C 304 TYR 0.015 0.001 TYR I 95 ARG 0.008 0.000 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 357 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 82 ASN cc_start: 0.8614 (m-40) cc_final: 0.8235 (m-40) REVERT: B 301 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8068 (pp) REVERT: C 25 MET cc_start: 0.7192 (mtm) cc_final: 0.6748 (mtm) REVERT: C 129 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7206 (pt0) REVERT: C 131 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7132 (p90) REVERT: C 283 GLU cc_start: 0.7441 (tp30) cc_final: 0.7124 (tp30) REVERT: E 50 ARG cc_start: 0.7908 (ptt180) cc_final: 0.7696 (ptt180) REVERT: E 264 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8815 (mt) REVERT: E 322 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: H 75 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8878 (p0) REVERT: H 89 ASP cc_start: 0.7904 (t70) cc_final: 0.7471 (t0) REVERT: H 230 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7514 (mt-10) REVERT: I 8 GLU cc_start: 0.7075 (pp20) cc_final: 0.6537 (pp20) REVERT: I 9 ILE cc_start: 0.8011 (mt) cc_final: 0.7338 (mt) REVERT: I 120 ASN cc_start: 0.8132 (m110) cc_final: 0.7625 (m110) REVERT: J 81 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7365 (mm-30) outliers start: 73 outliers final: 42 residues processed: 408 average time/residue: 0.3844 time to fit residues: 237.6404 Evaluate side-chains 354 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 305 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 308 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 283 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS B 114 HIS B 172 ASN C 77 GLN C 329 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN E 127 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 GLN F 329 ASN H 329 ASN I 21 HIS ** I 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 24729 Z= 0.350 Angle : 0.611 9.978 33691 Z= 0.319 Chirality : 0.043 0.191 3617 Planarity : 0.004 0.045 4314 Dihedral : 15.019 175.051 4346 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.54 % Favored : 91.43 % Rotamer: Outliers : 4.52 % Allowed : 20.03 % 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: -2.23 (0.14), residues: 3092 helix: -0.14 (0.17), residues: 954 sheet: -1.10 (0.23), residues: 493 loop : -2.51 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 30 HIS 0.010 0.001 HIS B 305 PHE 0.019 0.002 PHE G 95 TYR 0.018 0.002 TYR E 271 ARG 0.011 0.001 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 314 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 105 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8347 (pp) REVERT: B 301 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7926 (pp) REVERT: C 131 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7138 (p90) REVERT: C 329 ASN cc_start: 0.8458 (t0) cc_final: 0.7505 (t0) REVERT: D 87 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7034 (p0) REVERT: E 50 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7677 (ptt180) REVERT: E 264 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8870 (mt) REVERT: E 322 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: F 291 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7530 (mm-40) REVERT: G 19 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: G 45 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7535 (mtm110) REVERT: G 300 GLN cc_start: 0.7661 (mp10) cc_final: 0.7443 (mp10) REVERT: H 75 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.8987 (p0) REVERT: H 89 ASP cc_start: 0.8045 (t70) cc_final: 0.7597 (t0) REVERT: I 8 GLU cc_start: 0.7219 (pp20) cc_final: 0.6752 (pp20) REVERT: I 120 ASN cc_start: 0.8006 (m110) cc_final: 0.7403 (m110) REVERT: J 122 ARG cc_start: 0.7494 (tmt-80) cc_final: 0.7256 (tmt-80) outliers start: 99 outliers final: 57 residues processed: 382 average time/residue: 0.4059 time to fit residues: 234.8183 Evaluate side-chains 360 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 294 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 322 GLN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain I residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 286 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN B 64 HIS B 114 HIS ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 164 HIS E 127 ASN F 83 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN I 53 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24729 Z= 0.201 Angle : 0.539 13.164 33691 Z= 0.280 Chirality : 0.040 0.191 3617 Planarity : 0.004 0.045 4314 Dihedral : 14.839 176.410 4342 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.47 % Favored : 93.50 % Rotamer: Outliers : 4.33 % Allowed : 21.35 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 3092 helix: 0.32 (0.17), residues: 965 sheet: -0.85 (0.24), residues: 476 loop : -2.32 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 30 HIS 0.006 0.001 HIS B 305 PHE 0.014 0.001 PHE C 186 TYR 0.015 0.001 TYR I 95 ARG 0.006 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 317 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.3523 (OUTLIER) cc_final: 0.2977 (ttm) REVERT: L 10 ARG cc_start: 0.5588 (tpp80) cc_final: 0.5079 (ttp-170) REVERT: A 178 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 91 ASP cc_start: 0.6593 (OUTLIER) cc_final: 0.6118 (p0) REVERT: B 301 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8026 (pp) REVERT: C 131 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7116 (p90) REVERT: D 19 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7847 (p0) REVERT: D 87 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6894 (p0) REVERT: E 50 ARG cc_start: 0.7829 (ptt180) cc_final: 0.7548 (ptt180) REVERT: E 264 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8839 (mt) REVERT: G 45 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7544 (mtm110) REVERT: G 300 GLN cc_start: 0.7620 (mp10) cc_final: 0.7038 (mp10) REVERT: H 76 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8274 (mt) REVERT: H 89 ASP cc_start: 0.8013 (t70) cc_final: 0.7579 (t0) REVERT: H 91 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8654 (tp) REVERT: I 6 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5483 (tmm) REVERT: I 120 ASN cc_start: 0.8049 (m110) cc_final: 0.7573 (m110) outliers start: 95 outliers final: 59 residues processed: 377 average time/residue: 0.3845 time to fit residues: 220.9805 Evaluate side-chains 360 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 290 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 98 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 154 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS C 77 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24729 Z= 0.244 Angle : 0.556 12.246 33691 Z= 0.288 Chirality : 0.040 0.193 3617 Planarity : 0.004 0.051 4314 Dihedral : 14.703 175.701 4339 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.64 % Favored : 92.33 % Rotamer: Outliers : 4.74 % Allowed : 21.40 % Favored : 73.86 % 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: -1.58 (0.15), residues: 3092 helix: 0.60 (0.18), residues: 954 sheet: -0.76 (0.24), residues: 489 loop : -2.24 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 30 HIS 0.007 0.001 HIS B 305 PHE 0.013 0.001 PHE G 95 TYR 0.016 0.001 TYR I 95 ARG 0.009 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 299 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5454 (tpp80) cc_final: 0.5044 (ttp-170) REVERT: A 178 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8456 (mp) REVERT: B 91 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6190 (p0) REVERT: B 301 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8027 (pp) REVERT: C 131 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7067 (p90) REVERT: D 87 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.6897 (p0) REVERT: E 50 ARG cc_start: 0.7821 (ptt180) cc_final: 0.7527 (ptt180) REVERT: G 45 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7573 (mtm110) REVERT: G 300 GLN cc_start: 0.7572 (mp10) cc_final: 0.7208 (mp10) REVERT: H 76 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8367 (mt) REVERT: H 89 ASP cc_start: 0.8023 (t70) cc_final: 0.7586 (t0) REVERT: H 91 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8566 (tp) REVERT: I 9 ILE cc_start: 0.8220 (mt) cc_final: 0.8010 (mt) REVERT: I 120 ASN cc_start: 0.8040 (m110) cc_final: 0.7574 (m110) REVERT: J 1 MET cc_start: 0.6035 (tmm) cc_final: 0.5230 (mmt) outliers start: 104 outliers final: 68 residues processed: 373 average time/residue: 0.3787 time to fit residues: 216.5584 Evaluate side-chains 361 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 286 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 6.9990 chunk 273 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 303 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS A 262 ASN B 89 ASN B 114 HIS E 127 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24729 Z= 0.147 Angle : 0.501 10.698 33691 Z= 0.260 Chirality : 0.039 0.206 3617 Planarity : 0.003 0.044 4314 Dihedral : 14.575 176.751 4339 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.60 % Allowed : 22.72 % Favored : 73.68 % 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: -1.26 (0.15), residues: 3092 helix: 0.93 (0.18), residues: 954 sheet: -0.53 (0.24), residues: 477 loop : -2.10 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 30 HIS 0.004 0.001 HIS C 140 PHE 0.014 0.001 PHE B 321 TYR 0.014 0.001 TYR I 95 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 321 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5748 (tpp80) cc_final: 0.5353 (ttp-170) REVERT: A 178 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 131 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6973 (p90) REVERT: D 19 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7675 (p0) REVERT: D 87 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6811 (p0) REVERT: E 50 ARG cc_start: 0.7777 (ptt180) cc_final: 0.7524 (ptt180) REVERT: E 175 ARG cc_start: 0.7271 (ttm170) cc_final: 0.7058 (tpt170) REVERT: G 45 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7368 (mtm110) REVERT: H 76 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8068 (mt) REVERT: H 89 ASP cc_start: 0.7813 (t70) cc_final: 0.7425 (t0) REVERT: H 91 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8805 (tp) REVERT: I 120 ASN cc_start: 0.8047 (m110) cc_final: 0.7834 (m-40) REVERT: J 73 LYS cc_start: 0.7536 (pttp) cc_final: 0.7171 (pttp) outliers start: 79 outliers final: 52 residues processed: 376 average time/residue: 0.3930 time to fit residues: 227.3100 Evaluate side-chains 344 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 302 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 HIS B 114 HIS C 77 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 322 GLN H 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24729 Z= 0.167 Angle : 0.520 14.356 33691 Z= 0.267 Chirality : 0.039 0.283 3617 Planarity : 0.003 0.044 4314 Dihedral : 14.517 176.129 4337 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.01 % Allowed : 23.40 % Favored : 72.58 % 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: -1.09 (0.15), residues: 3092 helix: 1.08 (0.18), residues: 955 sheet: -0.46 (0.24), residues: 482 loop : -1.99 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 174 HIS 0.007 0.001 HIS A 203 PHE 0.029 0.001 PHE L 155 TYR 0.017 0.001 TYR I 95 ARG 0.007 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 304 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5826 (tpp80) cc_final: 0.5382 (ttp-170) REVERT: A 178 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 131 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6953 (p90) REVERT: D 19 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7705 (p0) REVERT: D 87 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7019 (p0) REVERT: E 50 ARG cc_start: 0.7788 (ptt180) cc_final: 0.7471 (ptt180) REVERT: E 302 LEU cc_start: 0.8634 (mt) cc_final: 0.8402 (mp) REVERT: G 45 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7392 (mtm110) REVERT: G 136 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6981 (ttp-170) REVERT: G 300 GLN cc_start: 0.7485 (mp10) cc_final: 0.7187 (mp10) REVERT: H 76 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8132 (mt) REVERT: H 89 ASP cc_start: 0.7878 (t70) cc_final: 0.7449 (t0) REVERT: I 9 ILE cc_start: 0.8205 (mt) cc_final: 0.7968 (pt) REVERT: I 69 GLU cc_start: 0.6687 (mt-10) cc_final: 0.6481 (mt-10) REVERT: I 120 ASN cc_start: 0.8041 (m110) cc_final: 0.7545 (m110) REVERT: J 6 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6846 (mmt) REVERT: J 73 LYS cc_start: 0.7504 (pttp) cc_final: 0.7239 (pttp) outliers start: 88 outliers final: 64 residues processed: 366 average time/residue: 0.3937 time to fit residues: 220.7402 Evaluate side-chains 364 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 293 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 149 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS C 77 GLN E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24729 Z= 0.196 Angle : 0.533 14.125 33691 Z= 0.274 Chirality : 0.040 0.334 3617 Planarity : 0.003 0.043 4314 Dihedral : 14.469 175.800 4337 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.61 % Allowed : 22.86 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3092 helix: 1.09 (0.18), residues: 965 sheet: -0.43 (0.24), residues: 481 loop : -1.97 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.005 0.001 HIS B 305 PHE 0.022 0.001 PHE L 155 TYR 0.018 0.001 TYR I 95 ARG 0.006 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 300 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5767 (tpp80) cc_final: 0.5381 (ttp-170) REVERT: A 178 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 131 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.7025 (p90) REVERT: C 159 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: D 19 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7737 (p0) REVERT: D 87 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7013 (p0) REVERT: G 45 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7392 (mtm110) REVERT: G 136 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6998 (ttp-170) REVERT: G 300 GLN cc_start: 0.7457 (mp10) cc_final: 0.7175 (mp10) REVERT: H 76 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8220 (mt) REVERT: H 89 ASP cc_start: 0.7857 (t70) cc_final: 0.7405 (t0) REVERT: I 120 ASN cc_start: 0.8015 (m110) cc_final: 0.7493 (m110) REVERT: J 6 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6758 (mmt) REVERT: J 122 ARG cc_start: 0.7465 (tmt-80) cc_final: 0.7159 (tmt-80) outliers start: 101 outliers final: 71 residues processed: 372 average time/residue: 0.3745 time to fit residues: 212.5280 Evaluate side-chains 366 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 287 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 264 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 266 optimal weight: 0.6980 chunk 281 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS C 77 GLN E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24729 Z= 0.167 Angle : 0.521 13.360 33691 Z= 0.268 Chirality : 0.039 0.308 3617 Planarity : 0.003 0.044 4314 Dihedral : 14.409 176.037 4337 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.65 % Allowed : 24.09 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 3092 helix: 1.18 (0.18), residues: 965 sheet: -0.36 (0.24), residues: 478 loop : -1.91 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 263 HIS 0.004 0.001 HIS A 200 PHE 0.039 0.001 PHE C 304 TYR 0.018 0.001 TYR I 95 ARG 0.007 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 307 time to evaluate : 2.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5760 (tpp80) cc_final: 0.5385 (ttp-170) REVERT: A 178 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 79 LYS cc_start: 0.8770 (mptt) cc_final: 0.8545 (mmtt) REVERT: C 131 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6986 (p90) REVERT: D 19 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7698 (p0) REVERT: D 87 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.7000 (p0) REVERT: E 46 GLU cc_start: 0.6852 (pt0) cc_final: 0.6636 (pt0) REVERT: E 50 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7357 (ptt180) REVERT: E 268 ASP cc_start: 0.8565 (p0) cc_final: 0.7739 (p0) REVERT: G 45 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7396 (mtm110) REVERT: G 136 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6918 (ttp-170) REVERT: G 300 GLN cc_start: 0.7454 (mp10) cc_final: 0.7219 (mp10) REVERT: H 76 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8137 (mt) REVERT: H 89 ASP cc_start: 0.7859 (t70) cc_final: 0.7426 (t0) REVERT: I 120 ASN cc_start: 0.7947 (m110) cc_final: 0.7431 (m110) REVERT: J 6 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6817 (mmt) REVERT: J 73 LYS cc_start: 0.7344 (pttp) cc_final: 0.6955 (pttm) outliers start: 80 outliers final: 64 residues processed: 361 average time/residue: 0.3500 time to fit residues: 191.1950 Evaluate side-chains 365 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 312 optimal weight: 40.0000 chunk 287 optimal weight: 0.0270 chunk 249 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 192 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24729 Z= 0.179 Angle : 0.534 15.822 33691 Z= 0.272 Chirality : 0.040 0.300 3617 Planarity : 0.003 0.044 4314 Dihedral : 14.399 175.646 4337 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.42 % Allowed : 24.45 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3092 helix: 1.22 (0.18), residues: 967 sheet: -0.34 (0.25), residues: 470 loop : -1.88 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 174 HIS 0.005 0.001 HIS B 305 PHE 0.036 0.001 PHE C 304 TYR 0.019 0.001 TYR I 95 ARG 0.007 0.000 ARG D 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6184 Ramachandran restraints generated. 3092 Oldfield, 0 Emsley, 3092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 298 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ARG cc_start: 0.5866 (tpp80) cc_final: 0.5499 (ttp-170) REVERT: L 117 MET cc_start: 0.4492 (mtt) cc_final: 0.3785 (mmm) REVERT: A 178 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 131 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6979 (p90) REVERT: D 19 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7722 (p0) REVERT: D 87 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7179 (p0) REVERT: E 46 GLU cc_start: 0.6861 (pt0) cc_final: 0.6641 (pt0) REVERT: E 50 ARG cc_start: 0.7736 (ptt180) cc_final: 0.7343 (ptt180) REVERT: E 268 ASP cc_start: 0.8595 (p0) cc_final: 0.7797 (p0) REVERT: G 45 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7407 (mtm110) REVERT: G 136 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6941 (ttp-170) REVERT: G 300 GLN cc_start: 0.7444 (mp10) cc_final: 0.7203 (mp10) REVERT: H 76 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8147 (mt) REVERT: H 89 ASP cc_start: 0.7864 (t70) cc_final: 0.7441 (t0) REVERT: I 120 ASN cc_start: 0.7942 (m110) cc_final: 0.7397 (m110) REVERT: J 6 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6837 (mmt) outliers start: 75 outliers final: 65 residues processed: 350 average time/residue: 0.3880 time to fit residues: 205.5689 Evaluate side-chains 366 residues out of total 2543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 294 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 263 TRP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 305 HIS Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 75 ASN Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain F residue 87 ASP Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 136 ARG Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain H residue 15 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 249 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 256 optimal weight: 0.8980 chunk 31 optimal weight: 40.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS E 127 ASN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 167 GLN H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.182805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143019 restraints weight = 32417.430| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.04 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24729 Z= 0.146 Angle : 0.523 15.500 33691 Z= 0.267 Chirality : 0.040 0.295 3617 Planarity : 0.003 0.046 4314 Dihedral : 14.355 175.911 4337 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.01 % Allowed : 24.86 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3092 helix: 1.30 (0.18), residues: 969 sheet: -0.27 (0.25), residues: 461 loop : -1.87 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 174 HIS 0.004 0.001 HIS C 140 PHE 0.034 0.001 PHE C 304 TYR 0.018 0.001 TYR I 95 ARG 0.007 0.000 ARG D 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5026.86 seconds wall clock time: 91 minutes 28.47 seconds (5488.47 seconds total)