Starting phenix.real_space_refine on Tue Mar 19 03:24:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ecw_31059/03_2024/7ecw_31059.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 69 5.49 5 S 27 5.16 5 C 14163 2.51 5 N 4253 2.21 5 O 4577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 321": "OE1" <-> "OE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "J GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23089 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 2251 Classifications: {'peptide': 424} Incomplete info: {'backbone_only': 266, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 399} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1200 Unresolved non-hydrogen angles: 1728 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 330 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 21, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 8, 'HIS:plan': 6, 'PHE:plan': 10, 'GLU:plan': 24, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 670 Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2364 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: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2264 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2554 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2534 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2569 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2556 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 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: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2552 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 989 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 928 Classifications: {'RNA': 44} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 18, 'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "N" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "O" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 12.21, per 1000 atoms: 0.53 Number of scatterers: 23089 At special positions: 0 Unit cell: (135.3, 134.2, 171.6, 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 27 16.00 P 69 15.00 O 4577 8.00 N 4253 7.00 C 14163 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: 9.37 Conformation dependent library (CDL) restraints added in 4.6 seconds 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 38 sheets defined 32.1% alpha, 19.4% beta 10 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 8.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.559A pdb=" N LEU A 100 " --> pdb=" O SER A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 123 removed outlier: 3.534A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 4.624A pdb=" N ASN A 132 " --> pdb=" O ASN A 129 " (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 196 through 211 removed outlier: 3.793A pdb=" N GLU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.736A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 314 through 341 removed outlier: 3.806A pdb=" N ILE A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 385 through 399 removed outlier: 4.295A pdb=" N ASN A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 398 " --> pdb=" O TRP A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.080A pdb=" N GLN A 413 " --> pdb=" O PRO A 409 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 418 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'B' and resid 33 through 53 removed outlier: 4.000A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N SER B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 removed outlier: 3.569A pdb=" N ILE B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 177 Processing helix chain 'B' and resid 178 through 181 removed outlier: 4.057A pdb=" N LEU B 181 " --> pdb=" O ARG B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.847A pdb=" N ASP B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 207 through 212' Processing helix chain 'B' and resid 291 through 295 removed outlier: 4.009A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.757A pdb=" N ASP B 300 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.873A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 144 removed outlier: 3.611A pdb=" N ALA C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.787A pdb=" N GLY C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.776A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 319 through 329 removed outlier: 3.768A pdb=" N TYR C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 removed outlier: 3.837A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.929A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.649A pdb=" N ARG D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.742A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.821A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 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 332 removed outlier: 4.343A pdb=" N VAL D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.875A pdb=" N SER E 36 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 73 removed outlier: 4.169A pdb=" N ILE E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 129 removed outlier: 3.977A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 144 removed outlier: 3.971A pdb=" N ARG E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.937A pdb=" N ALA E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.693A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.550A pdb=" N LEU E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP E 309 " --> pdb=" O TYR E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.792A pdb=" N HIS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 326 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 removed outlier: 3.732A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 70 removed outlier: 3.562A pdb=" N ASP F 68 " --> pdb=" O PRO F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.250A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.843A pdb=" N LEU F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.583A pdb=" N ILE F 260 " --> pdb=" O HIS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 313 Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.868A pdb=" N HIS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F 333 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 removed outlier: 4.042A pdb=" N ASP G 68 " --> pdb=" O PRO G 64 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.705A pdb=" N ASN G 141 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.893A pdb=" N LEU G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 205 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 263 removed outlier: 3.502A pdb=" N ALA G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 313 removed outlier: 3.508A pdb=" N ASP G 309 " --> pdb=" O TYR G 305 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 313 " --> pdb=" O ASP G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 removed outlier: 3.845A pdb=" N HIS G 324 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL G 326 " --> pdb=" O GLN G 322 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 327 " --> pdb=" O GLN G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.607A pdb=" N SER H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 72 removed outlier: 3.748A pdb=" N GLN H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 removed outlier: 3.591A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 191 through 204 removed outlier: 3.936A pdb=" N LEU H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 removed outlier: 3.722A pdb=" N ILE H 260 " --> pdb=" O HIS H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 313 removed outlier: 3.722A pdb=" N LEU H 307 " --> pdb=" O ASP H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 333 removed outlier: 3.991A pdb=" N TYR H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL H 326 " --> pdb=" O GLN H 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 327 " --> pdb=" O GLN H 323 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY H 333 " --> pdb=" O ASN H 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 75 Processing helix chain 'I' and resid 109 through 121 Processing helix chain 'J' and resid 3 through 12 Processing helix chain 'J' and resid 21 through 30 Processing helix chain 'J' and resid 42 through 56 removed outlier: 3.969A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 75 Processing helix chain 'J' and resid 109 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 21 removed outlier: 5.323A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N SER B 108 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N CYS B 63 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU B 110 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 61 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY B 112 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 59 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 14.042A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TRP B 316 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 313 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 14 removed outlier: 3.695A pdb=" N LEU C 12 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.688A pdb=" N ALA C 157 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 4.593A pdb=" N ALA C 253 " --> pdb=" O MET C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 47 removed outlier: 4.564A pdb=" N ARG C 45 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 81 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.609A pdb=" N ALA D 108 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA D 157 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 172 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.603A pdb=" N ARG D 98 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D 28 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.744A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.753A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.800A pdb=" N ASP D 268 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.526A pdb=" N LEU E 12 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.957A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 172 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.547A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA E 253 " --> pdb=" O MET E 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 49 removed outlier: 7.737A pdb=" N THR E 78 " --> pdb=" O SER E 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.689A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 12 " --> pdb=" O PHE F 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.844A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA F 157 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL F 158 " --> pdb=" O ASP F 177 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP F 177 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 160 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG F 175 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE F 162 " --> pdb=" O THR F 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR F 173 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS F 164 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.501A pdb=" N ALA F 23 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA F 253 " --> pdb=" O MET F 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 44 through 51 removed outlier: 4.110A pdb=" N PHE I 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR F 78 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 11.528A pdb=" N CYS I 106 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 14.996A pdb=" N ASP F 80 " --> pdb=" O CYS I 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR I 102 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER I 96 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE I 104 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS I 94 " --> pdb=" O PHE I 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD1, first strand: chain 'G' and resid 108 through 109 Processing sheet with id=AD2, first strand: chain 'G' and resid 18 through 20 removed outlier: 4.167A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.573A pdb=" N LEU G 24 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA G 253 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA G 252 " --> pdb=" O VAL G 249 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 45 through 51 removed outlier: 4.068A pdb=" N ASN G 75 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU G 76 " --> pdb=" O GLN G 241 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AD6, first strand: chain 'G' and resid 287 through 288 removed outlier: 3.648A pdb=" N LYS G 293 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 108 through 109 removed outlier: 3.524A pdb=" N ALA H 108 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 334 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA H 157 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL H 158 " --> pdb=" O ASP H 177 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP H 177 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL H 160 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG H 175 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 162 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.594A pdb=" N ASP H 19 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG H 98 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY H 28 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.637A pdb=" N PHE J 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N THR H 78 " --> pdb=" O PHE J 104 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N CYS J 106 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP H 80 " --> pdb=" O CYS J 106 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR J 102 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER J 96 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE J 104 " --> pdb=" O LYS J 94 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS J 94 " --> pdb=" O PHE J 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.637A pdb=" N ASP H 268 " --> pdb=" O ILE H 280 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 10.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4386 1.32 - 1.45: 6167 1.45 - 1.57: 12936 1.57 - 1.69: 136 1.69 - 1.81: 39 Bond restraints: 23664 Sorted by residual: bond pdb=" N ILE E 232 " pdb=" CA ILE E 232 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.64e+00 bond pdb=" N LEU A 268 " pdb=" CA LEU A 268 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.95e+00 bond pdb=" N GLN E 241 " pdb=" CA GLN E 241 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.91e+00 bond pdb=" N LEU E 233 " pdb=" CA LEU E 233 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N LEU E 231 " pdb=" CA LEU E 231 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.56e+00 ... (remaining 23659 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.21: 626 105.21 - 112.57: 11789 112.57 - 119.92: 8648 119.92 - 127.28: 10883 127.28 - 134.64: 353 Bond angle restraints: 32299 Sorted by residual: angle pdb=" O3' DG N 33 " pdb=" C3' DG N 33 " pdb=" C2' DG N 33 " ideal model delta sigma weight residual 111.50 99.38 12.12 1.50e+00 4.44e-01 6.53e+01 angle pdb=" N GLY G 240 " pdb=" CA GLY G 240 " pdb=" C GLY G 240 " ideal model delta sigma weight residual 115.32 123.37 -8.05 1.38e+00 5.25e-01 3.40e+01 angle pdb=" N VAL F 249 " pdb=" CA VAL F 249 " pdb=" C VAL F 249 " ideal model delta sigma weight residual 109.34 97.85 11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N LEU G 233 " pdb=" CA LEU G 233 " pdb=" C LEU G 233 " ideal model delta sigma weight residual 111.36 117.29 -5.93 1.09e+00 8.42e-01 2.96e+01 angle pdb=" N VAL G 249 " pdb=" CA VAL G 249 " pdb=" C VAL G 249 " ideal model delta sigma weight residual 109.34 98.26 11.08 2.08e+00 2.31e-01 2.84e+01 ... (remaining 32294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 13048 31.19 - 62.39: 668 62.39 - 93.58: 83 93.58 - 124.78: 0 124.78 - 155.97: 2 Dihedral angle restraints: 13801 sinusoidal: 5875 harmonic: 7926 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 44.03 155.97 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 72.47 127.53 1 1.50e+01 4.44e-03 6.87e+01 dihedral pdb=" CA LEU B 12 " pdb=" C LEU B 12 " pdb=" N PRO B 13 " pdb=" CA PRO B 13 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 13798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2993 0.075 - 0.151: 423 0.151 - 0.226: 61 0.226 - 0.301: 4 0.301 - 0.377: 3 Chirality restraints: 3484 Sorted by residual: chirality pdb=" CA HIS B 305 " pdb=" N HIS B 305 " pdb=" C HIS B 305 " pdb=" CB HIS B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C3' DG N 33 " pdb=" C4' DG N 33 " pdb=" O3' DG N 33 " pdb=" C2' DG N 33 " both_signs ideal model delta sigma weight residual False -2.66 -3.01 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ALA G 319 " pdb=" N ALA G 319 " pdb=" C ALA G 319 " pdb=" CB ALA G 319 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 3481 not shown) Planarity restraints: 4078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 232 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ILE G 232 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE G 232 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU G 233 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 127 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ASN C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU C 128 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 228 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.30e+00 pdb=" N PRO A 229 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.038 5.00e-02 4.00e+02 ... (remaining 4075 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 111 2.54 - 3.13: 15611 3.13 - 3.72: 33173 3.72 - 4.31: 47071 4.31 - 4.90: 79839 Nonbonded interactions: 175805 Sorted by model distance: nonbonded pdb=" O ASN G 75 " pdb=" OD1 ASN G 75 " model vdw 1.950 3.040 nonbonded pdb=" OD1 ASP H 111 " pdb=" N ALA H 112 " model vdw 2.174 2.520 nonbonded pdb=" O LEU B 139 " pdb=" O2 U M 2 " model vdw 2.202 3.040 nonbonded pdb=" CG1 VAL A 199 " pdb=" NH1 ARG A 258 " model vdw 2.218 3.540 nonbonded pdb=" O VAL I 36 " pdb=" OD1 ASP I 37 " model vdw 2.270 3.040 ... (remaining 175800 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 230 or (resid 231 and (name N or name CA or name \ C or name O or name CB )) or resid 244 through 272 or (resid 273 through 275 an \ d (name N or name CA or name C or name O or name CB )) or resid 276 through 337 \ or (resid 338 and (name N or name CA or name C or name O )))) selection = (chain 'D' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 231 or re \ sid 244 through 323 or (resid 324 and (name N or name CA or name C or name O or \ name CB )) or resid 325 through 337 or (resid 338 and (name N or name CA or name \ C or name O )))) selection = (chain 'E' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'F' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'G' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 337 or (resid 338 and (name N or name CA or name C or nam \ e O )))) selection = (chain 'H' and (resid 6 through 48 or resid 77 through 183 or (resid 184 and (na \ me N or name CA or name C or name O or name CB )) or resid 185 through 230 or (r \ esid 231 and (name N or name CA or name C or name O or name CB )) or resid 244 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 338)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.680 Set scattering table: 0.280 Process input model: 67.410 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.007 0.080 23664 Z= 0.440 Angle : 0.887 12.122 32299 Z= 0.511 Chirality : 0.056 0.377 3484 Planarity : 0.006 0.068 4078 Dihedral : 17.659 155.975 8869 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.81 % Rotamer: Outliers : 1.10 % Allowed : 14.77 % Favored : 84.13 % Cbeta Deviations : 0.04 % 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: -3.73 (0.12), residues: 2906 helix: -3.20 (0.11), residues: 880 sheet: -0.28 (0.25), residues: 445 loop : -2.77 (0.12), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 30 HIS 0.009 0.002 HIS A 188 PHE 0.019 0.002 PHE B 66 TYR 0.021 0.002 TYR H 285 ARG 0.005 0.001 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 314 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 PHE cc_start: 0.7192 (p90) cc_final: 0.6719 (p90) REVERT: A 225 GLN cc_start: 0.6663 (mm-40) cc_final: 0.6309 (tp-100) REVERT: A 237 ASN cc_start: 0.8555 (p0) cc_final: 0.8272 (p0) REVERT: B 110 LEU cc_start: 0.8178 (pp) cc_final: 0.7817 (mt) REVERT: B 218 ARG cc_start: 0.5786 (ptm160) cc_final: 0.4799 (ttt-90) REVERT: C 150 ARG cc_start: 0.6423 (mtp-110) cc_final: 0.5804 (mmp80) REVERT: C 161 ARG cc_start: 0.6574 (ttm110) cc_final: 0.5948 (tpt-90) REVERT: D 16 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8246 (ptp90) REVERT: D 208 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.5693 (p90) REVERT: D 291 GLN cc_start: 0.7900 (tt0) cc_final: 0.7659 (tt0) REVERT: E 241 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6773 (tp40) REVERT: G 159 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: G 260 ILE cc_start: 0.8681 (pt) cc_final: 0.8222 (mt) REVERT: G 285 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 23 outliers final: 10 residues processed: 332 average time/residue: 0.4694 time to fit residues: 220.0061 Evaluate side-chains 247 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 16 ARG Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.0470 chunk 224 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 188 HIS B 19 ASN B 45 GLN B 82 ASN B 269 ASN B 293 HIS B 305 HIS C 83 ASN C 140 HIS C 163 ASN C 167 GLN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN E 163 ASN E 229 GLN E 291 GLN E 310 ASN F 110 ASN F 129 GLN F 163 ASN F 241 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 310 ASN H 77 GLN H 223 GLN H 241 GLN I 14 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23664 Z= 0.144 Angle : 0.523 10.660 32299 Z= 0.282 Chirality : 0.040 0.219 3484 Planarity : 0.004 0.055 4078 Dihedral : 15.431 155.567 4177 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 2.58 % Allowed : 17.45 % Favored : 79.97 % 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: -2.21 (0.14), residues: 2906 helix: -1.12 (0.16), residues: 882 sheet: 0.30 (0.25), residues: 453 loop : -2.28 (0.13), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 174 HIS 0.005 0.001 HIS C 164 PHE 0.030 0.001 PHE A 232 TYR 0.013 0.001 TYR C 271 ARG 0.006 0.000 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 2.776 Fit side-chains REVERT: A 225 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6258 (tp-100) REVERT: A 247 LYS cc_start: 0.8425 (mmmm) cc_final: 0.8118 (mmmm) REVERT: B 59 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 218 ARG cc_start: 0.5799 (ptm160) cc_final: 0.4840 (ttt-90) REVERT: C 150 ARG cc_start: 0.6206 (mtp-110) cc_final: 0.5516 (mmp80) REVERT: C 161 ARG cc_start: 0.6402 (ttm110) cc_final: 0.5765 (tpt-90) REVERT: D 208 HIS cc_start: 0.7084 (OUTLIER) cc_final: 0.5419 (p90) REVERT: D 291 GLN cc_start: 0.7908 (tt0) cc_final: 0.7566 (tt0) REVERT: E 184 ARG cc_start: 0.7276 (mmt-90) cc_final: 0.7076 (mmt180) REVERT: E 241 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6650 (tp40) REVERT: F 175 ARG cc_start: 0.7670 (ttt180) cc_final: 0.7458 (ttt180) REVERT: F 283 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7301 (mt-10) REVERT: F 297 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: G 129 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6754 (pt0) REVERT: G 159 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: G 285 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: H 148 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8127 (pp) REVERT: H 329 ASN cc_start: 0.7458 (p0) cc_final: 0.6980 (t0) outliers start: 54 outliers final: 29 residues processed: 287 average time/residue: 0.4418 time to fit residues: 184.5547 Evaluate side-chains 253 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 74 optimal weight: 30.0000 chunk 269 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 216 optimal weight: 0.0470 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 114 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 291 GLN F 129 GLN G 129 GLN G 144 ASN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23664 Z= 0.307 Angle : 0.622 10.998 32299 Z= 0.327 Chirality : 0.043 0.219 3484 Planarity : 0.005 0.051 4078 Dihedral : 15.292 154.870 4158 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 4.21 % Allowed : 18.50 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.15), residues: 2906 helix: -0.40 (0.17), residues: 888 sheet: 0.48 (0.25), residues: 451 loop : -2.18 (0.14), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 30 HIS 0.007 0.001 HIS H 164 PHE 0.031 0.002 PHE A 232 TYR 0.018 0.002 TYR H 285 ARG 0.004 0.001 ARG F 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 216 time to evaluate : 2.758 Fit side-chains REVERT: A 225 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6252 (tp-100) REVERT: A 247 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8037 (mmmm) REVERT: B 100 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8365 (pt0) REVERT: B 218 ARG cc_start: 0.5849 (ptm160) cc_final: 0.4988 (ttp-170) REVERT: C 150 ARG cc_start: 0.6501 (mtp-110) cc_final: 0.5804 (mmp80) REVERT: C 151 ASN cc_start: 0.5939 (m-40) cc_final: 0.5518 (m110) REVERT: C 161 ARG cc_start: 0.6465 (ttm110) cc_final: 0.6179 (tpt-90) REVERT: C 250 ARG cc_start: 0.3237 (OUTLIER) cc_final: 0.2496 (ptt180) REVERT: D 208 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.5876 (p90) REVERT: D 297 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: E 241 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6715 (tp40) REVERT: F 283 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7218 (mt-10) REVERT: F 297 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: G 16 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8577 (ptt90) REVERT: G 80 ASP cc_start: 0.8334 (m-30) cc_final: 0.8123 (m-30) REVERT: G 129 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: H 34 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: H 128 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6795 (tm-30) REVERT: H 148 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8325 (pp) REVERT: H 219 ILE cc_start: 0.8854 (tt) cc_final: 0.8584 (tt) REVERT: H 229 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: I 12 ASN cc_start: 0.6626 (p0) cc_final: 0.6313 (p0) outliers start: 88 outliers final: 53 residues processed: 289 average time/residue: 0.4228 time to fit residues: 178.3734 Evaluate side-chains 265 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 GLN E 291 GLN F 129 GLN G 129 GLN H 163 ASN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23664 Z= 0.234 Angle : 0.561 9.626 32299 Z= 0.298 Chirality : 0.041 0.215 3484 Planarity : 0.004 0.049 4078 Dihedral : 15.105 153.858 4155 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 3.78 % Allowed : 19.93 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 2906 helix: 0.04 (0.18), residues: 894 sheet: 0.81 (0.26), residues: 423 loop : -2.09 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 30 HIS 0.004 0.001 HIS H 164 PHE 0.033 0.001 PHE A 232 TYR 0.016 0.002 TYR F 285 ARG 0.004 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 212 time to evaluate : 2.610 Fit side-chains REVERT: A 225 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6315 (tp-100) REVERT: B 218 ARG cc_start: 0.5804 (ptm160) cc_final: 0.5271 (ttm-80) REVERT: C 150 ARG cc_start: 0.6386 (mtp-110) cc_final: 0.5753 (mmp80) REVERT: C 151 ASN cc_start: 0.6007 (m-40) cc_final: 0.5518 (m110) REVERT: C 161 ARG cc_start: 0.6420 (ttm110) cc_final: 0.6196 (tpt-90) REVERT: D 208 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.5786 (p90) REVERT: D 291 GLN cc_start: 0.7989 (tt0) cc_final: 0.7543 (tt0) REVERT: D 297 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: D 322 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7507 (pp30) REVERT: E 241 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6730 (tp40) REVERT: F 297 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: G 16 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8558 (ptt90) REVERT: G 80 ASP cc_start: 0.8254 (m-30) cc_final: 0.7968 (m-30) REVERT: G 129 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: G 285 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: H 148 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8322 (pp) REVERT: H 219 ILE cc_start: 0.8762 (tt) cc_final: 0.8466 (tt) REVERT: H 229 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8647 (pt0) REVERT: I 12 ASN cc_start: 0.6591 (p0) cc_final: 0.6231 (p0) outliers start: 79 outliers final: 51 residues processed: 275 average time/residue: 0.4130 time to fit residues: 166.1419 Evaluate side-chains 264 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 203 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 322 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 60.0000 chunk 146 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 291 GLN F 129 GLN G 129 GLN I 14 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23664 Z= 0.288 Angle : 0.602 10.176 32299 Z= 0.318 Chirality : 0.043 0.217 3484 Planarity : 0.004 0.051 4078 Dihedral : 15.010 153.395 4155 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 4.40 % Allowed : 19.84 % Favored : 75.76 % 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: 2906 helix: 0.26 (0.18), residues: 888 sheet: 0.81 (0.26), residues: 429 loop : -2.06 (0.14), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 30 HIS 0.005 0.001 HIS H 164 PHE 0.031 0.002 PHE A 232 TYR 0.018 0.002 TYR C 271 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 208 time to evaluate : 2.330 Fit side-chains REVERT: A 225 GLN cc_start: 0.7147 (mm-40) cc_final: 0.6281 (tp-100) REVERT: A 247 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8174 (mmmm) REVERT: B 69 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: B 218 ARG cc_start: 0.5849 (ptm160) cc_final: 0.5041 (ttp-170) REVERT: C 150 ARG cc_start: 0.6416 (mtp-110) cc_final: 0.5841 (mmp80) REVERT: C 151 ASN cc_start: 0.6104 (m-40) cc_final: 0.5659 (m110) REVERT: C 161 ARG cc_start: 0.6476 (ttm110) cc_final: 0.6222 (ttt-90) REVERT: C 250 ARG cc_start: 0.3311 (OUTLIER) cc_final: 0.2449 (ptt180) REVERT: D 291 GLN cc_start: 0.7978 (tt0) cc_final: 0.7503 (tt0) REVERT: D 297 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: E 241 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6787 (tp40) REVERT: F 297 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: G 16 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8560 (ptt90) REVERT: G 285 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: H 148 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8340 (pp) REVERT: H 175 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7916 (ttp-110) REVERT: H 219 ILE cc_start: 0.8819 (tt) cc_final: 0.8516 (tt) REVERT: H 229 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8697 (pt0) REVERT: I 12 ASN cc_start: 0.6906 (p0) cc_final: 0.6540 (p0) outliers start: 92 outliers final: 64 residues processed: 288 average time/residue: 0.3998 time to fit residues: 169.4081 Evaluate side-chains 270 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 197 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 140 HIS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 9 ILE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 237 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 0.0670 chunk 150 optimal weight: 0.0980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 GLN F 129 GLN G 129 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23664 Z= 0.119 Angle : 0.478 9.245 32299 Z= 0.256 Chirality : 0.038 0.212 3484 Planarity : 0.003 0.050 4078 Dihedral : 14.782 151.996 4155 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 21.70 % Favored : 75.57 % 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: -0.79 (0.16), residues: 2906 helix: 0.77 (0.18), residues: 887 sheet: 0.85 (0.25), residues: 447 loop : -1.80 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 29 HIS 0.003 0.000 HIS G 324 PHE 0.012 0.001 PHE G 14 TYR 0.014 0.001 TYR F 285 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 223 time to evaluate : 2.682 Fit side-chains REVERT: A 211 PHE cc_start: 0.7318 (p90) cc_final: 0.6991 (p90) REVERT: A 225 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6319 (tp-100) REVERT: B 218 ARG cc_start: 0.5718 (ptm160) cc_final: 0.4963 (ttp-170) REVERT: C 151 ASN cc_start: 0.6171 (m-40) cc_final: 0.5645 (m-40) REVERT: D 291 GLN cc_start: 0.7811 (tt0) cc_final: 0.7438 (tt0) REVERT: E 241 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6748 (tp40) REVERT: E 329 ASN cc_start: 0.8000 (p0) cc_final: 0.7706 (p0) REVERT: F 22 ASP cc_start: 0.7757 (m-30) cc_final: 0.7488 (m-30) REVERT: G 80 ASP cc_start: 0.8131 (m-30) cc_final: 0.7814 (m-30) REVERT: G 129 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6427 (pt0) REVERT: H 148 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8285 (pp) REVERT: H 219 ILE cc_start: 0.8703 (tt) cc_final: 0.8389 (pt) REVERT: H 229 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8652 (pt0) outliers start: 57 outliers final: 31 residues processed: 266 average time/residue: 0.4146 time to fit residues: 163.7975 Evaluate side-chains 252 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 5.9990 chunk 32 optimal weight: 40.0000 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 178 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN F 129 GLN G 129 GLN I 87 HIS ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23664 Z= 0.187 Angle : 0.524 9.125 32299 Z= 0.277 Chirality : 0.040 0.219 3484 Planarity : 0.004 0.044 4078 Dihedral : 14.712 152.401 4153 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.01 % Allowed : 21.65 % Favored : 75.33 % 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: -0.68 (0.16), residues: 2906 helix: 0.87 (0.18), residues: 889 sheet: 0.96 (0.26), residues: 441 loop : -1.76 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 147 HIS 0.004 0.001 HIS H 164 PHE 0.013 0.001 PHE G 14 TYR 0.015 0.001 TYR C 271 ARG 0.005 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 209 time to evaluate : 2.516 Fit side-chains REVERT: A 225 GLN cc_start: 0.7125 (mm-40) cc_final: 0.6306 (tp-100) REVERT: B 218 ARG cc_start: 0.5781 (ptm160) cc_final: 0.5047 (ttp-170) REVERT: C 151 ASN cc_start: 0.6198 (m-40) cc_final: 0.5725 (m-40) REVERT: D 291 GLN cc_start: 0.7920 (tt0) cc_final: 0.7444 (tt0) REVERT: D 314 ARG cc_start: 0.7590 (mtm110) cc_final: 0.7384 (mtm180) REVERT: E 241 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6798 (tp40) REVERT: E 285 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: F 297 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: G 80 ASP cc_start: 0.8195 (m-30) cc_final: 0.7910 (m-30) REVERT: G 260 ILE cc_start: 0.8574 (pt) cc_final: 0.8297 (mt) REVERT: G 285 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: H 148 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8296 (pp) REVERT: H 219 ILE cc_start: 0.8714 (tt) cc_final: 0.8410 (tt) outliers start: 63 outliers final: 48 residues processed: 258 average time/residue: 0.4072 time to fit residues: 155.8906 Evaluate side-chains 252 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 170 optimal weight: 0.0870 chunk 85 optimal weight: 0.0010 chunk 56 optimal weight: 0.1980 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 0.0060 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN G 129 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23664 Z= 0.129 Angle : 0.480 9.151 32299 Z= 0.256 Chirality : 0.039 0.216 3484 Planarity : 0.003 0.043 4078 Dihedral : 14.586 152.024 4153 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.82 % Allowed : 21.80 % Favored : 75.38 % 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: -0.52 (0.16), residues: 2906 helix: 1.03 (0.18), residues: 896 sheet: 0.98 (0.25), residues: 442 loop : -1.65 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 174 HIS 0.003 0.000 HIS G 324 PHE 0.022 0.001 PHE J 43 TYR 0.013 0.001 TYR F 285 ARG 0.006 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 2.562 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6304 (tp-100) REVERT: B 218 ARG cc_start: 0.5722 (ptm160) cc_final: 0.5010 (ttp-170) REVERT: C 151 ASN cc_start: 0.6267 (m-40) cc_final: 0.5830 (m-40) REVERT: E 241 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6633 (tp40) REVERT: E 285 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: E 329 ASN cc_start: 0.8299 (p0) cc_final: 0.7888 (p0) REVERT: G 80 ASP cc_start: 0.8131 (m-30) cc_final: 0.7835 (m-30) REVERT: H 148 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8266 (pp) REVERT: H 219 ILE cc_start: 0.8707 (tt) cc_final: 0.8359 (pt) outliers start: 59 outliers final: 46 residues processed: 261 average time/residue: 0.4058 time to fit residues: 156.5086 Evaluate side-chains 256 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 207 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 140 HIS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 249 optimal weight: 0.0170 chunk 265 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 0.0010 chunk 240 optimal weight: 7.9990 chunk 251 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 overall best weight: 1.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN G 129 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23664 Z= 0.189 Angle : 0.524 9.134 32299 Z= 0.277 Chirality : 0.040 0.220 3484 Planarity : 0.003 0.044 4078 Dihedral : 14.595 152.466 4153 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.87 % Allowed : 21.99 % Favored : 75.14 % 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: -0.53 (0.16), residues: 2906 helix: 0.96 (0.18), residues: 901 sheet: 0.98 (0.25), residues: 451 loop : -1.64 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 30 HIS 0.004 0.001 HIS H 164 PHE 0.013 0.001 PHE G 14 TYR 0.015 0.001 TYR C 271 ARG 0.005 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 2.270 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6296 (tp-100) REVERT: B 69 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: B 218 ARG cc_start: 0.5764 (ptm160) cc_final: 0.5007 (ttp-170) REVERT: E 241 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6672 (tp40) REVERT: E 285 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: G 16 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8685 (ptt90) REVERT: G 32 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: G 80 ASP cc_start: 0.8191 (m-30) cc_final: 0.7908 (m-30) REVERT: G 129 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6799 (pt0) REVERT: G 260 ILE cc_start: 0.8578 (pt) cc_final: 0.8286 (mt) REVERT: G 285 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: H 148 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8314 (pp) REVERT: H 219 ILE cc_start: 0.8723 (tt) cc_final: 0.8407 (tt) outliers start: 60 outliers final: 44 residues processed: 244 average time/residue: 0.3993 time to fit residues: 144.4191 Evaluate side-chains 248 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 129 GLN Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 171 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 195 optimal weight: 0.0870 chunk 294 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN G 129 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23664 Z= 0.165 Angle : 0.506 8.872 32299 Z= 0.269 Chirality : 0.040 0.218 3484 Planarity : 0.003 0.044 4078 Dihedral : 14.554 152.505 4151 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.72 % Allowed : 22.23 % Favored : 75.05 % 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: -0.51 (0.16), residues: 2906 helix: 0.99 (0.18), residues: 902 sheet: 1.01 (0.25), residues: 451 loop : -1.64 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 30 HIS 0.004 0.001 HIS C 164 PHE 0.013 0.001 PHE I 68 TYR 0.014 0.001 TYR C 271 ARG 0.006 0.000 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 2.880 Fit side-chains revert: symmetry clash REVERT: A 225 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6289 (tp-100) REVERT: B 27 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8678 (mp) REVERT: B 69 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: B 218 ARG cc_start: 0.5709 (ptm160) cc_final: 0.5060 (ttp-170) REVERT: E 241 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6574 (tp40) REVERT: E 285 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: F 297 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: G 16 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8691 (ptt90) REVERT: G 32 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7713 (mp10) REVERT: G 80 ASP cc_start: 0.8175 (m-30) cc_final: 0.7891 (m-30) REVERT: G 260 ILE cc_start: 0.8526 (pt) cc_final: 0.8239 (mt) REVERT: G 285 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: H 148 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8311 (pp) REVERT: H 219 ILE cc_start: 0.8695 (tt) cc_final: 0.8380 (tt) outliers start: 57 outliers final: 43 residues processed: 246 average time/residue: 0.4032 time to fit residues: 147.3032 Evaluate side-chains 248 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 196 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 131 PHE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 117 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 16 ARG Chi-restraints excluded: chain G residue 19 ASP Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 110 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 336 PHE Chi-restraints excluded: chain I residue 77 SER Chi-restraints excluded: chain J residue 47 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 216 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 29 optimal weight: 40.0000 chunk 43 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS C 140 HIS ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN E 291 GLN ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.180388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141124 restraints weight = 27491.321| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.23 r_work: 0.3126 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23664 Z= 0.128 Angle : 0.477 9.207 32299 Z= 0.254 Chirality : 0.039 0.218 3484 Planarity : 0.003 0.044 4078 Dihedral : 14.399 152.491 4151 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.63 % Allowed : 22.42 % Favored : 74.95 % 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: -0.35 (0.16), residues: 2906 helix: 1.18 (0.18), residues: 902 sheet: 1.06 (0.26), residues: 442 loop : -1.55 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 174 HIS 0.003 0.000 HIS C 164 PHE 0.022 0.001 PHE J 43 TYR 0.013 0.001 TYR C 271 ARG 0.006 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4835.53 seconds wall clock time: 87 minutes 28.17 seconds (5248.17 seconds total)