Starting phenix.real_space_refine on Sat Oct 31 07:34:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.cif Found real_map, /net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.map" model { file = "/net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11lc_75794/10_2026/11lc_75794.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 25746 2.51 5 N 6792 2.21 5 O 7588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40272 Number of models: 1 Model: "" Number of chains: 16 Chain: "AJ" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1684 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "AY" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2086 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 17, 'TRANS': 250} Chain: "Ah" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5225 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "Ao" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2659 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 306} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Ap" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 343} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3635 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 25, 'TRANS': 417} Chain breaks: 3 Chain: "M" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2200 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2200 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "O" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2200 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2200 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2200 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "h" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2204 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "i" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2204 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "j" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2204 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "k" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2204 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "l" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2204 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 8.41, per 1000 atoms: 0.21 Number of scatterers: 40272 At special positions: 0 Unit cell: (183.75, 271.95, 216.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 7588 8.00 N 6792 7.00 C 25746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAo 109 " - pdb=" SG CYSAo 153 " distance=2.02 Simple disulfide: pdb=" SG CYSAp 109 " - pdb=" SG CYSAp 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9630 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 43 sheets defined 48.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'AJ' and resid 58 through 64 removed outlier: 3.590A pdb=" N ASNAJ 62 " --> pdb=" O ARGAJ 59 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 66 through 81 Processing helix chain 'AJ' and resid 131 through 145 removed outlier: 3.697A pdb=" N LEUAJ 144 " --> pdb=" O TRPAJ 140 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 154 through 159 removed outlier: 4.194A pdb=" N ILEAJ 158 " --> pdb=" O METAJ 154 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VALAJ 159 " --> pdb=" O LEUAJ 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'AJ' and resid 154 through 159' Processing helix chain 'AJ' and resid 231 through 244 Processing helix chain 'AY' and resid 11 through 17 removed outlier: 3.607A pdb=" N ALAAY 15 " --> pdb=" O GLYAY 12 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SERAY 17 " --> pdb=" O GLYAY 14 " (cutoff:3.500A) Processing helix chain 'AY' and resid 58 through 64 Processing helix chain 'AY' and resid 66 through 81 removed outlier: 3.776A pdb=" N VALAY 81 " --> pdb=" O LEUAY 77 " (cutoff:3.500A) Processing helix chain 'AY' and resid 128 through 130 No H-bonds generated for 'chain 'AY' and resid 128 through 130' Processing helix chain 'AY' and resid 131 through 145 Processing helix chain 'AY' and resid 154 through 159 removed outlier: 4.324A pdb=" N ILEAY 158 " --> pdb=" O METAY 154 " (cutoff:3.500A) Processing helix chain 'AY' and resid 168 through 173 removed outlier: 4.135A pdb=" N SERAY 173 " --> pdb=" O ASPAY 170 " (cutoff:3.500A) Processing helix chain 'AY' and resid 231 through 244 removed outlier: 3.565A pdb=" N ARGAY 240 " --> pdb=" O ALAAY 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEUAY 241 " --> pdb=" O PHEAY 237 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSAY 244 " --> pdb=" O ARGAY 240 " (cutoff:3.500A) Processing helix chain 'AY' and resid 251 through 255 Processing helix chain 'AY' and resid 263 through 268 Processing helix chain 'Ah' and resid 55 through 61 Processing helix chain 'Ah' and resid 62 through 66 Processing helix chain 'Ah' and resid 73 through 86 removed outlier: 4.096A pdb=" N LEUAh 77 " --> pdb=" O SERAh 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILEAh 78 " --> pdb=" O PROAh 74 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 196 through 199 removed outlier: 3.919A pdb=" N ASPAh 199 " --> pdb=" O ALAAh 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 196 through 199' Processing helix chain 'Ah' and resid 217 through 225 removed outlier: 3.710A pdb=" N ILEAh 221 " --> pdb=" O ARGAh 217 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 273 through 277 removed outlier: 3.526A pdb=" N VALAh 277 " --> pdb=" O PHEAh 274 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 279 through 283 removed outlier: 3.676A pdb=" N GLUAh 283 " --> pdb=" O ASPAh 280 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 303 through 319 removed outlier: 3.839A pdb=" N LYSAh 319 " --> pdb=" O GLUAh 315 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 380 through 394 Processing helix chain 'Ah' and resid 419 through 425 Processing helix chain 'Ah' and resid 428 through 433 removed outlier: 4.096A pdb=" N LEUAh 432 " --> pdb=" O ASNAh 428 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARGAh 433 " --> pdb=" O VALAh 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ah' and resid 428 through 433' Processing helix chain 'Ah' and resid 451 through 466 Processing helix chain 'Ah' and resid 467 through 469 No H-bonds generated for 'chain 'Ah' and resid 467 through 469' Processing helix chain 'Ah' and resid 502 through 515 removed outlier: 4.054A pdb=" N VALAh 506 " --> pdb=" O LEUAh 502 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 546 through 557 Processing helix chain 'Ah' and resid 583 through 586 Processing helix chain 'Ah' and resid 587 through 607 removed outlier: 3.599A pdb=" N VALAh 591 " --> pdb=" O SERAh 587 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLUAh 607 " --> pdb=" O ARGAh 603 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 615 through 631 Processing helix chain 'Ao' and resid 162 through 172 removed outlier: 4.177A pdb=" N ALAAo 171 " --> pdb=" O ILEAo 167 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYSAo 172 " --> pdb=" O GLUAo 168 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 195 through 218 removed outlier: 4.003A pdb=" N CYSAo 211 " --> pdb=" O ALAAo 207 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HISAo 212 " --> pdb=" O LEUAo 208 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALAAo 213 " --> pdb=" O GLYAo 209 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 237 through 246 Processing helix chain 'Ao' and resid 267 through 271 removed outlier: 3.543A pdb=" N ALAAo 270 " --> pdb=" O ASNAo 267 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 274 through 282 Processing helix chain 'Ao' and resid 283 through 288 Processing helix chain 'Ao' and resid 310 through 314 Processing helix chain 'Ao' and resid 374 through 380 removed outlier: 3.816A pdb=" N TYRAo 378 " --> pdb=" O THRAo 374 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 385 through 397 Processing helix chain 'Ao' and resid 401 through 411 Processing helix chain 'Ao' and resid 412 through 415 Processing helix chain 'Ao' and resid 416 through 437 Proline residue: Ao 425 - end of helix removed outlier: 3.648A pdb=" N ILEAo 436 " --> pdb=" O ARGAo 432 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 72 through 76 removed outlier: 3.605A pdb=" N GLUAp 75 " --> pdb=" O ASPAp 72 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 162 through 170 Processing helix chain 'Ap' and resid 196 through 218 removed outlier: 3.802A pdb=" N CYSAp 211 " --> pdb=" O ALAAp 207 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N HISAp 212 " --> pdb=" O LEUAp 208 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALAAp 213 " --> pdb=" O GLYAp 209 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 237 through 246 Processing helix chain 'Ap' and resid 267 through 271 Processing helix chain 'Ap' and resid 274 through 282 Processing helix chain 'Ap' and resid 283 through 288 Processing helix chain 'Ap' and resid 310 through 314 Processing helix chain 'Ap' and resid 374 through 379 Processing helix chain 'Ap' and resid 385 through 396 Processing helix chain 'Ap' and resid 401 through 411 Processing helix chain 'Ap' and resid 412 through 415 Processing helix chain 'Ap' and resid 416 through 436 Proline residue: Ap 425 - end of helix removed outlier: 3.570A pdb=" N ILEAp 436 " --> pdb=" O ARGAp 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 15 through 32 Processing helix chain 'D' and resid 129 through 146 removed outlier: 4.063A pdb=" N ALA D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.966A pdb=" N VAL D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 297 through 304 removed outlier: 3.983A pdb=" N ASP D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.709A pdb=" N LEU D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 367 removed outlier: 3.759A pdb=" N LEU D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 451 through 463 Processing helix chain 'D' and resid 465 through 469 removed outlier: 4.107A pdb=" N TRP D 469 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 490 removed outlier: 3.511A pdb=" N ILE D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 27 Processing helix chain 'M' and resid 32 through 46 removed outlier: 3.601A pdb=" N VAL M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 107 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 136 through 152 removed outlier: 3.544A pdb=" N THR M 151 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG M 152 " --> pdb=" O ALA M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 Processing helix chain 'M' and resid 178 through 188 Processing helix chain 'M' and resid 191 through 210 Processing helix chain 'M' and resid 225 through 240 Processing helix chain 'M' and resid 253 through 264 removed outlier: 3.801A pdb=" N LEU M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 265 through 268 removed outlier: 4.172A pdb=" N SER M 268 " --> pdb=" O GLY M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 278 through 283 Processing helix chain 'M' and resid 305 through 315 Processing helix chain 'N' and resid 9 through 27 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 92 through 107 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 136 through 152 removed outlier: 4.222A pdb=" N ARG N 152 " --> pdb=" O ALA N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 162 Processing helix chain 'N' and resid 178 through 188 Processing helix chain 'N' and resid 191 through 210 Processing helix chain 'N' and resid 225 through 240 Processing helix chain 'N' and resid 253 through 261 removed outlier: 3.733A pdb=" N LEU N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 267 removed outlier: 3.956A pdb=" N GLY N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) Processing helix chain 'N' and resid 278 through 283 Processing helix chain 'N' and resid 305 through 315 Processing helix chain 'O' and resid 9 through 27 Processing helix chain 'O' and resid 32 through 46 Processing helix chain 'O' and resid 92 through 107 Processing helix chain 'O' and resid 113 through 134 Processing helix chain 'O' and resid 136 through 152 removed outlier: 4.016A pdb=" N ARG O 152 " --> pdb=" O ALA O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 163 Processing helix chain 'O' and resid 178 through 188 Processing helix chain 'O' and resid 191 through 210 Processing helix chain 'O' and resid 225 through 240 Processing helix chain 'O' and resid 253 through 261 removed outlier: 3.707A pdb=" N LEU O 261 " --> pdb=" O GLU O 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 268 removed outlier: 4.051A pdb=" N GLY O 265 " --> pdb=" O PRO O 262 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA O 267 " --> pdb=" O LEU O 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER O 268 " --> pdb=" O GLY O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 278 through 283 Processing helix chain 'O' and resid 305 through 315 Processing helix chain 'P' and resid 9 through 27 removed outlier: 3.522A pdb=" N LEU P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG P 20 " --> pdb=" O ALA P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 46 Processing helix chain 'P' and resid 92 through 107 Processing helix chain 'P' and resid 113 through 134 Processing helix chain 'P' and resid 136 through 152 removed outlier: 3.502A pdb=" N THR P 151 " --> pdb=" O LEU P 147 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG P 152 " --> pdb=" O ALA P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 154 through 162 Processing helix chain 'P' and resid 178 through 188 Processing helix chain 'P' and resid 191 through 210 Processing helix chain 'P' and resid 225 through 240 Processing helix chain 'P' and resid 253 through 261 removed outlier: 3.695A pdb=" N LEU P 261 " --> pdb=" O GLU P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 262 through 268 removed outlier: 4.146A pdb=" N GLY P 265 " --> pdb=" O PRO P 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA P 267 " --> pdb=" O LEU P 264 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER P 268 " --> pdb=" O GLY P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 278 through 283 Processing helix chain 'P' and resid 305 through 315 Processing helix chain 'Q' and resid 9 through 27 removed outlier: 4.083A pdb=" N VAL Q 14 " --> pdb=" O THR Q 10 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA Q 26 " --> pdb=" O TYR Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 47 removed outlier: 3.694A pdb=" N PHE Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 113 through 134 Processing helix chain 'Q' and resid 136 through 150 removed outlier: 3.911A pdb=" N LYS Q 150 " --> pdb=" O ALA Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 154 through 162 Processing helix chain 'Q' and resid 178 through 188 Processing helix chain 'Q' and resid 191 through 210 Processing helix chain 'Q' and resid 225 through 239 removed outlier: 3.580A pdb=" N ILE Q 229 " --> pdb=" O ASN Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 253 through 261 Processing helix chain 'Q' and resid 262 through 267 removed outlier: 3.844A pdb=" N GLY Q 265 " --> pdb=" O PRO Q 262 " (cutoff:3.500A) Processing helix chain 'Q' and resid 278 through 283 Processing helix chain 'Q' and resid 305 through 315 removed outlier: 3.544A pdb=" N LEU Q 309 " --> pdb=" O ASN Q 305 " (cutoff:3.500A) Processing helix chain 'h' and resid 7 through 27 Processing helix chain 'h' and resid 32 through 47 removed outlier: 3.925A pdb=" N PHE h 36 " --> pdb=" O SER h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 92 through 107 Processing helix chain 'h' and resid 108 through 111 Processing helix chain 'h' and resid 114 through 134 Processing helix chain 'h' and resid 136 through 150 removed outlier: 3.617A pdb=" N THR h 149 " --> pdb=" O VAL h 145 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS h 150 " --> pdb=" O ALA h 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 154 through 162 removed outlier: 3.840A pdb=" N LEU h 158 " --> pdb=" O ASP h 154 " (cutoff:3.500A) Processing helix chain 'h' and resid 178 through 189 Processing helix chain 'h' and resid 191 through 209 Processing helix chain 'h' and resid 226 through 240 Processing helix chain 'h' and resid 255 through 261 Processing helix chain 'h' and resid 262 through 265 removed outlier: 4.151A pdb=" N GLY h 265 " --> pdb=" O PRO h 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 262 through 265' Processing helix chain 'h' and resid 279 through 283 Processing helix chain 'h' and resid 305 through 315 removed outlier: 3.536A pdb=" N LEU h 309 " --> pdb=" O ASN h 305 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG h 314 " --> pdb=" O TYR h 310 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 27 Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.986A pdb=" N PHE i 36 " --> pdb=" O SER i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 107 Processing helix chain 'i' and resid 108 through 111 Processing helix chain 'i' and resid 115 through 134 Processing helix chain 'i' and resid 136 through 150 removed outlier: 3.527A pdb=" N THR i 149 " --> pdb=" O VAL i 145 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS i 150 " --> pdb=" O ALA i 146 " (cutoff:3.500A) Processing helix chain 'i' and resid 154 through 162 Processing helix chain 'i' and resid 178 through 189 Processing helix chain 'i' and resid 191 through 209 Processing helix chain 'i' and resid 225 through 240 removed outlier: 4.487A pdb=" N ILE i 229 " --> pdb=" O ASN i 225 " (cutoff:3.500A) Processing helix chain 'i' and resid 255 through 261 Processing helix chain 'i' and resid 262 through 265 removed outlier: 4.356A pdb=" N GLY i 265 " --> pdb=" O PRO i 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 262 through 265' Processing helix chain 'i' and resid 305 through 315 removed outlier: 3.582A pdb=" N VAL i 313 " --> pdb=" O LEU i 309 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG i 314 " --> pdb=" O TYR i 310 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 27 Processing helix chain 'j' and resid 32 through 47 removed outlier: 4.058A pdb=" N PHE j 36 " --> pdb=" O SER j 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 92 through 107 Processing helix chain 'j' and resid 108 through 111 Processing helix chain 'j' and resid 114 through 134 Processing helix chain 'j' and resid 136 through 150 Processing helix chain 'j' and resid 154 through 162 Processing helix chain 'j' and resid 178 through 189 Processing helix chain 'j' and resid 191 through 209 Processing helix chain 'j' and resid 225 through 240 removed outlier: 4.357A pdb=" N ILE j 229 " --> pdb=" O ASN j 225 " (cutoff:3.500A) Processing helix chain 'j' and resid 255 through 261 Processing helix chain 'j' and resid 279 through 283 removed outlier: 3.632A pdb=" N MET j 282 " --> pdb=" O SER j 279 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA j 283 " --> pdb=" O ALA j 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 279 through 283' Processing helix chain 'j' and resid 305 through 315 removed outlier: 3.608A pdb=" N LEU j 309 " --> pdb=" O ASN j 305 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG j 314 " --> pdb=" O TYR j 310 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 27 Processing helix chain 'k' and resid 32 through 47 removed outlier: 3.887A pdb=" N PHE k 36 " --> pdb=" O SER k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 107 Processing helix chain 'k' and resid 108 through 111 Processing helix chain 'k' and resid 114 through 134 Processing helix chain 'k' and resid 136 through 151 removed outlier: 3.630A pdb=" N THR k 151 " --> pdb=" O LEU k 147 " (cutoff:3.500A) Processing helix chain 'k' and resid 154 through 162 Processing helix chain 'k' and resid 178 through 189 Processing helix chain 'k' and resid 191 through 209 Processing helix chain 'k' and resid 225 through 240 removed outlier: 4.560A pdb=" N ILE k 229 " --> pdb=" O ASN k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 255 through 261 Processing helix chain 'k' and resid 279 through 283 removed outlier: 4.116A pdb=" N ALA k 283 " --> pdb=" O ALA k 280 " (cutoff:3.500A) Processing helix chain 'k' and resid 306 through 315 removed outlier: 4.321A pdb=" N ARG k 314 " --> pdb=" O TYR k 310 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 27 Processing helix chain 'l' and resid 33 through 47 Processing helix chain 'l' and resid 92 through 107 Processing helix chain 'l' and resid 115 through 134 Processing helix chain 'l' and resid 136 through 150 removed outlier: 3.571A pdb=" N LYS l 150 " --> pdb=" O ALA l 146 " (cutoff:3.500A) Processing helix chain 'l' and resid 154 through 162 Processing helix chain 'l' and resid 178 through 189 Processing helix chain 'l' and resid 191 through 209 Processing helix chain 'l' and resid 225 through 239 removed outlier: 3.596A pdb=" N PHE l 236 " --> pdb=" O GLU l 232 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU l 237 " --> pdb=" O ILE l 233 " (cutoff:3.500A) Processing helix chain 'l' and resid 255 through 261 Processing helix chain 'l' and resid 279 through 283 removed outlier: 4.607A pdb=" N ALA l 283 " --> pdb=" O ALA l 280 " (cutoff:3.500A) Processing helix chain 'l' and resid 305 through 315 removed outlier: 3.647A pdb=" N VAL l 313 " --> pdb=" O LEU l 309 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG l 314 " --> pdb=" O TYR l 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AJ' and resid 51 through 56 removed outlier: 6.708A pdb=" N THRAJ 175 " --> pdb=" O LEUAJ 55 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALAAJ 174 " --> pdb=" O ASNAJ 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYSAJ 194 " --> pdb=" O METAJ 176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEUAJ 193 " --> pdb=" O GLNAJ 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AJ' and resid 93 through 97 removed outlier: 5.401A pdb=" N VALAJ 97 " --> pdb=" O VALAJ 111 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VALAJ 111 " --> pdb=" O VALAJ 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AJ' and resid 100 through 101 removed outlier: 4.108A pdb=" N GLUAJ 106 " --> pdb=" O VALAJ 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AJ' and resid 122 through 126 Processing sheet with id=AA5, first strand: chain 'AY' and resid 51 through 56 removed outlier: 6.513A pdb=" N THRAY 175 " --> pdb=" O LEUAY 55 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALAAY 174 " --> pdb=" O ASNAY 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AY' and resid 84 through 86 removed outlier: 3.948A pdb=" N SERAY 84 " --> pdb=" O GLYAY 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AY' and resid 93 through 100 removed outlier: 6.801A pdb=" N GLUAY 93 " --> pdb=" O VALAY 114 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VALAY 114 " --> pdb=" O GLUAY 93 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLUAY 95 " --> pdb=" O SERAY 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ah' and resid 36 through 39 Processing sheet with id=AA9, first strand: chain 'Ah' and resid 169 through 174 removed outlier: 4.001A pdb=" N SERAh 181 " --> pdb=" O GLYAh 171 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLNAh 298 " --> pdb=" O LEUAh 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ah' and resid 169 through 174 removed outlier: 4.001A pdb=" N SERAh 181 " --> pdb=" O GLYAh 171 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N SERAh 181 " --> pdb=" O ALAAh 112 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ALAAh 112 " --> pdb=" O SERAh 181 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYRAh 183 " --> pdb=" O VALAh 110 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VALAh 110 " --> pdb=" O TYRAh 183 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VALAh 108 " --> pdb=" O PROAh 185 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEUAh 187 " --> pdb=" O ILEAh 106 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYSAh 140 " --> pdb=" O VALAh 117 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N GLUAh 352 " --> pdb=" O ASPAh 143 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEUAh 145 " --> pdb=" O GLUAh 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ah' and resid 244 through 245 Processing sheet with id=AB3, first strand: chain 'Ah' and resid 244 through 245 removed outlier: 3.566A pdb=" N PHEAh 369 " --> pdb=" O ILEAh 203 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ah' and resid 264 through 265 removed outlier: 3.742A pdb=" N THRAh 270 " --> pdb=" O GLNAh 265 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Ah' and resid 412 through 413 removed outlier: 6.705A pdb=" N VALAh 413 " --> pdb=" O ILEAh 439 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N SERAh 441 " --> pdb=" O VALAh 413 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALAAh 483 " --> pdb=" O ILEAh 438 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ah' and resid 499 through 501 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 562 through 563 removed outlier: 3.535A pdb=" N GLNAh 562 " --> pdb=" O PHEAh 570 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ah' and resid 640 through 646 removed outlier: 3.948A pdb=" N THRAh 640 " --> pdb=" O ILEAh 665 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILEAh 665 " --> pdb=" O THRAh 640 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYSAh 642 " --> pdb=" O SERAh 663 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SERAh 663 " --> pdb=" O LYSAh 642 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGAh 644 " --> pdb=" O ASPAh 661 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYRAh 646 " --> pdb=" O HISAh 659 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ao' and resid 51 through 56 removed outlier: 6.068A pdb=" N TYRAo 53 " --> pdb=" O ARGAo 82 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ARGAo 82 " --> pdb=" O TYRAo 53 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLUAo 55 " --> pdb=" O ARGAo 80 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARGAo 80 " --> pdb=" O GLUAo 55 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYRAo 78 " --> pdb=" O GLUAo 175 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N THRAo 177 " --> pdb=" O TYRAo 78 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARGAo 80 " --> pdb=" O THRAo 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ao' and resid 122 through 126 removed outlier: 3.644A pdb=" N TYRAo 135 " --> pdb=" O LEUAo 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ao' and resid 219 through 220 Processing sheet with id=AC3, first strand: chain 'Ao' and resid 294 through 298 Processing sheet with id=AC4, first strand: chain 'Ap' and resid 95 through 97 removed outlier: 3.540A pdb=" N ARGAp 102 " --> pdb=" O ASPAp 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Ap' and resid 109 through 110 removed outlier: 3.679A pdb=" N ASPAp 154 " --> pdb=" O ARGAp 139 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARGAp 139 " --> pdb=" O ASPAp 154 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SERAp 156 " --> pdb=" O ILEAp 137 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILEAp 137 " --> pdb=" O SERAp 156 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLNAp 158 " --> pdb=" O TYRAp 135 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYRAp 135 " --> pdb=" O GLNAp 158 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILEAp 160 " --> pdb=" O ALAAp 133 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALAAp 133 " --> pdb=" O ILEAp 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Ap' and resid 219 through 220 removed outlier: 3.541A pdb=" N THRAp 225 " --> pdb=" O SERAp 220 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Ap' and resid 235 through 236 removed outlier: 7.580A pdb=" N TYRAp 236 " --> pdb=" O METAp 320 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.808A pdb=" N LEU D 4 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 261 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 259 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS D 258 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 109 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.743A pdb=" N PHE D 247 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 245 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 243 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 223 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP D 254 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N GLU D 221 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 151 through 160 removed outlier: 6.565A pdb=" N ALA D 151 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 223 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU D 153 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 219 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N GLU D 221 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP D 254 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 223 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 244 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 338 through 345 removed outlier: 6.732A pdb=" N LEU D 431 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR D 343 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 429 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU D 345 " --> pdb=" O TYR D 427 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N TYR D 427 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 432 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 392 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 409 Processing sheet with id=AD4, first strand: chain 'M' and resid 217 through 221 removed outlier: 6.531A pdb=" N ARG M 218 " --> pdb=" O ILE M 321 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG M 323 " --> pdb=" O ARG M 218 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL M 220 " --> pdb=" O ARG M 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'N' and resid 220 through 221 removed outlier: 6.714A pdb=" N VAL N 220 " --> pdb=" O ARG N 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'N' and resid 249 through 250 removed outlier: 7.126A pdb=" N TYR N 249 " --> pdb=" O LYS N 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'O' and resid 220 through 221 removed outlier: 6.694A pdb=" N VAL O 220 " --> pdb=" O ARG O 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'P' and resid 220 through 221 removed outlier: 6.574A pdb=" N VAL P 220 " --> pdb=" O ARG P 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'Q' and resid 217 through 221 removed outlier: 3.863A pdb=" N ARG Q 218 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR Q 298 " --> pdb=" O LEU Q 320 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE Q 322 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER Q 300 " --> pdb=" O PHE Q 322 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 274 through 276 removed outlier: 4.552A pdb=" N GLN Q 274 " --> pdb=" O PHE l 276 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE l 276 " --> pdb=" O GLN Q 274 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE Q 276 " --> pdb=" O GLN l 274 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN l 274 " --> pdb=" O PHE Q 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'h' and resid 300 through 301 removed outlier: 6.421A pdb=" N SER h 300 " --> pdb=" O PHE h 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'i' and resid 220 through 221 removed outlier: 6.893A pdb=" N VAL i 220 " --> pdb=" O ARG i 323 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER i 300 " --> pdb=" O PHE i 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'j' and resid 220 through 221 removed outlier: 6.594A pdb=" N VAL j 220 " --> pdb=" O ARG j 323 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER j 300 " --> pdb=" O PHE j 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'k' and resid 168 through 169 Processing sheet with id=AE6, first strand: chain 'k' and resid 220 through 221 removed outlier: 6.697A pdb=" N VAL k 220 " --> pdb=" O ARG k 323 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER k 300 " --> pdb=" O PHE k 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'l' and resid 220 through 221 removed outlier: 6.745A pdb=" N VAL l 220 " --> pdb=" O ARG l 323 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER l 300 " --> pdb=" O PHE l 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 1769 hydrogen bonds defined for protein. 5088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.63 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.49: 23735 1.49 - 1.76: 17142 1.76 - 2.03: 253 2.03 - 2.30: 0 2.30 - 2.57: 2 Bond restraints: 41132 Sorted by residual: bond pdb=" CD2 TYR D 89 " pdb=" CE2 TYR D 89 " ideal model delta sigma weight residual 1.382 2.567 -1.185 3.00e-02 1.11e+03 1.56e+03 bond pdb=" CD1 TYR D 89 " pdb=" CE1 TYR D 89 " ideal model delta sigma weight residual 1.382 2.369 -0.987 3.00e-02 1.11e+03 1.08e+03 bond pdb=" CB HISAJ 83 " pdb=" CG HISAJ 83 " ideal model delta sigma weight residual 1.497 1.910 -0.413 1.40e-02 5.10e+03 8.69e+02 bond pdb=" CE1 TYR D 89 " pdb=" CZ TYR D 89 " ideal model delta sigma weight residual 1.378 1.924 -0.546 2.40e-02 1.74e+03 5.18e+02 bond pdb=" CE2 TYR D 89 " pdb=" CZ TYR D 89 " ideal model delta sigma weight residual 1.378 1.912 -0.534 2.40e-02 1.74e+03 4.95e+02 ... (remaining 41127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 55842 3.85 - 7.71: 79 7.71 - 11.56: 8 11.56 - 15.41: 1 15.41 - 19.27: 1 Bond angle restraints: 55931 Sorted by residual: angle pdb=" CA HISAJ 83 " pdb=" CB HISAJ 83 " pdb=" CG HISAJ 83 " ideal model delta sigma weight residual 113.80 133.07 -19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" ND1 HISAJ 83 " pdb=" CG HISAJ 83 " pdb=" CD2 HISAJ 83 " ideal model delta sigma weight residual 106.10 98.97 7.13 1.00e+00 1.00e+00 5.08e+01 angle pdb=" N HISAJ 83 " pdb=" CA HISAJ 83 " pdb=" CB HISAJ 83 " ideal model delta sigma weight residual 110.98 117.04 -6.06 1.32e+00 5.74e-01 2.11e+01 angle pdb=" CB HISAJ 83 " pdb=" CG HISAJ 83 " pdb=" ND1 HISAJ 83 " ideal model delta sigma weight residual 122.70 129.45 -6.75 1.50e+00 4.44e-01 2.02e+01 angle pdb=" C GLY j 316 " pdb=" N LEU j 317 " pdb=" CA LEU j 317 " ideal model delta sigma weight residual 121.80 131.82 -10.02 2.44e+00 1.68e-01 1.69e+01 ... (remaining 55926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 23223 17.75 - 35.50: 1262 35.50 - 53.25: 262 53.25 - 70.99: 57 70.99 - 88.74: 5 Dihedral angle restraints: 24809 sinusoidal: 9900 harmonic: 14909 Sorted by residual: dihedral pdb=" CA TYR D 320 " pdb=" C TYR D 320 " pdb=" N PRO D 321 " pdb=" CA PRO D 321 " ideal model delta harmonic sigma weight residual -180.00 -135.87 -44.13 0 5.00e+00 4.00e-02 7.79e+01 dihedral pdb=" CA ASN Q 241 " pdb=" C ASN Q 241 " pdb=" N PRO Q 242 " pdb=" CA PRO Q 242 " ideal model delta harmonic sigma weight residual 180.00 146.28 33.72 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA ASNAh 529 " pdb=" C ASNAh 529 " pdb=" N PROAh 530 " pdb=" CA PROAh 530 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 24806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4514 0.031 - 0.062: 1254 0.062 - 0.093: 393 0.093 - 0.124: 183 0.124 - 0.155: 8 Chirality restraints: 6352 Sorted by residual: chirality pdb=" CA HISAJ 83 " pdb=" N HISAJ 83 " pdb=" C HISAJ 83 " pdb=" CB HISAJ 83 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE D 490 " pdb=" N ILE D 490 " pdb=" C ILE D 490 " pdb=" CB ILE D 490 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VALAo 49 " pdb=" N VALAo 49 " pdb=" C VALAo 49 " pdb=" CB VALAo 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 6349 not shown) Planarity restraints: 7175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 89 " 0.014 2.00e-02 2.50e+03 2.91e-02 1.69e+01 pdb=" CG TYR D 89 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 89 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR D 89 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR D 89 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR D 89 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR D 89 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR D 89 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 320 " 0.057 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO D 321 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HISAJ 83 " 0.007 2.00e-02 2.50e+03 1.91e-02 5.49e+00 pdb=" CG HISAJ 83 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HISAJ 83 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 HISAJ 83 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HISAJ 83 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HISAJ 83 " -0.007 2.00e-02 2.50e+03 ... (remaining 7172 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 740 2.66 - 3.22: 38999 3.22 - 3.78: 61987 3.78 - 4.34: 79044 4.34 - 4.90: 123335 Nonbonded interactions: 304105 Sorted by model distance: nonbonded pdb=" CG HISAJ 83 " pdb=" CE2 TYR D 89 " model vdw 2.094 3.560 nonbonded pdb=" O TYRAo 371 " pdb=" OH TYRAo 378 " model vdw 2.104 3.040 nonbonded pdb=" O LEUAJ 247 " pdb=" OH TYR D 278 " model vdw 2.120 3.040 nonbonded pdb=" ND1 HISAJ 83 " pdb=" CD2 TYR D 89 " model vdw 2.133 3.420 nonbonded pdb=" O ALA Q 146 " pdb=" OG1 THR Q 149 " model vdw 2.139 3.040 ... (remaining 304100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'Ao' and (resid 50 through 180 or resid 195 through 438)) selection = (chain 'Ap' and (resid 50 through 58 or resid 77 through 88 or resid 107 through \ 143 or resid 150 through 438)) } ncs_group { reference = (chain 'M' and (resid 8 through 47 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 or (resid 213 through 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 316 or (resid 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 325)) selection = (chain 'N' and (resid 8 through 47 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 or (resid 213 through 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 316 or (resid 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 325)) selection = (chain 'O' and (resid 8 through 47 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 or (resid 213 through 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 316 or (resid 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 325)) selection = (chain 'P' and (resid 8 through 47 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 or (resid 213 through 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 316 or (resid 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 325)) selection = (chain 'Q' and (resid 8 through 47 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 or (resid 213 through 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 267 \ or (resid 268 and (name N or name CA or name C or name O or name CB )) or resid \ 269 through 316 or (resid 317 and (name N or name CA or name C or name O or nam \ e CB )) or resid 318 through 325)) selection = (chain 'h' and (resid 8 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 288 or (resid 289 and (name N or \ name CA or name C or name O or name CB )) or resid 290 through 325)) selection = (chain 'i' and (resid 8 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 288 or (resid 289 and (name N or \ name CA or name C or name O or name CB )) or resid 290 through 325)) selection = (chain 'j' and (resid 8 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 288 or (resid 289 and (name N or \ name CA or name C or name O or name CB )) or resid 290 through 325)) selection = (chain 'k' and (resid 8 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 288 or (resid 289 and (name N or \ name CA or name C or name O or name CB )) or resid 290 through 325)) selection = (chain 'l' and (resid 8 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 288 or (resid 289 and (name N or \ name CA or name C or name O or name CB )) or resid 290 through 325)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 23.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 32.960 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.010 1.185 41134 Z= 0.386 Angle : 0.539 19.267 55935 Z= 0.301 Chirality : 0.035 0.155 6352 Planarity : 0.004 0.088 7175 Dihedral : 11.566 88.742 15173 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.87 % Favored : 92.95 % Rotamer: Outliers : 4.87 % Allowed : 8.74 % Favored : 86.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.12), residues: 4976 helix: 2.36 (0.11), residues: 2256 sheet: -1.13 (0.25), residues: 461 loop : -1.99 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 292 TYR 0.054 0.001 TYR D 89 PHE 0.009 0.001 PHEAJ 254 TRP 0.012 0.001 TRP h 116 HIS 0.027 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.39 (41132) covalent geometry : angle 0.53894 / 0.30 (55931) SS BOND : bond 0.00535 / 0.28 ( 2) SS BOND : angle 1.10392 / 0.65 ( 4) hydrogen bonds : bond 0.17337 / 11.79 ( 1761) hydrogen bonds : angle 5.51860 / 3.90 ( 5088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 698 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 73 TYR cc_start: 0.9492 (t80) cc_final: 0.7141 (m-10) REVERT: AJ 75 LYS cc_start: 0.9438 (tttt) cc_final: 0.8667 (ttpt) REVERT: AJ 113 ASP cc_start: 0.8860 (t0) cc_final: 0.8405 (t0) REVERT: AJ 123 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: AJ 126 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: AJ 139 GLN cc_start: 0.9376 (tt0) cc_final: 0.9161 (tm-30) REVERT: AJ 145 LEU cc_start: 0.9496 (mt) cc_final: 0.9155 (mt) REVERT: AJ 178 PHE cc_start: 0.8992 (m-80) cc_final: 0.8708 (m-80) REVERT: AJ 190 ASN cc_start: 0.8850 (m-40) cc_final: 0.8292 (t0) REVERT: AJ 197 MET cc_start: 0.8141 (mpt) cc_final: 0.7106 (mpt) REVERT: AJ 204 ASP cc_start: 0.9111 (m-30) cc_final: 0.8880 (m-30) REVERT: AJ 220 LEU cc_start: 0.9488 (mt) cc_final: 0.9182 (tt) REVERT: AJ 223 GLN cc_start: 0.9131 (tt0) cc_final: 0.8492 (tt0) REVERT: AJ 244 LYS cc_start: 0.9513 (mptt) cc_final: 0.9239 (tttt) REVERT: AY 95 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9207 (pm20) REVERT: AY 115 LYS cc_start: 0.9156 (mttt) cc_final: 0.8912 (tptt) REVERT: AY 125 ILE cc_start: 0.9714 (mt) cc_final: 0.9450 (mp) REVERT: AY 145 LEU cc_start: 0.9714 (mt) cc_final: 0.9315 (mt) REVERT: AY 198 MET cc_start: 0.9424 (mtt) cc_final: 0.8754 (mpp) REVERT: AY 242 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9274 (tp) REVERT: Ah 51 LEU cc_start: 0.9585 (mt) cc_final: 0.9068 (tp) REVERT: Ah 305 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8751 (p0) REVERT: Ah 432 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8827 (pt) REVERT: Ah 461 MET cc_start: 0.8771 (tmm) cc_final: 0.8326 (tmm) REVERT: Ah 615 ASP cc_start: 0.8840 (t0) cc_final: 0.8620 (t0) REVERT: Ao 118 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8867 (tp) REVERT: Ao 202 ASP cc_start: 0.9491 (m-30) cc_final: 0.9160 (t0) REVERT: Ao 206 ARG cc_start: 0.9448 (mtt-85) cc_final: 0.8667 (mtt180) REVERT: Ao 259 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7558 (p90) REVERT: Ao 407 GLN cc_start: 0.9175 (tt0) cc_final: 0.8868 (pt0) REVERT: Ap 131 ARG cc_start: 0.9010 (ptp-110) cc_final: 0.8707 (ptp-170) REVERT: Ap 206 ARG cc_start: 0.9155 (mtt-85) cc_final: 0.8806 (mmm-85) REVERT: Ap 227 LEU cc_start: 0.9076 (mp) cc_final: 0.8843 (tt) REVERT: Ap 384 MET cc_start: 0.6435 (mtt) cc_final: 0.6148 (pmm) REVERT: Ap 390 MET cc_start: 0.9536 (mtp) cc_final: 0.9158 (mtm) REVERT: Ap 394 MET cc_start: 0.9617 (ttp) cc_final: 0.8979 (mmp) REVERT: Ap 422 TYR cc_start: 0.9183 (m-80) cc_final: 0.8965 (m-80) REVERT: D 1 MET cc_start: 0.0953 (mtt) cc_final: 0.0082 (mtt) REVERT: D 30 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9155 (tp) REVERT: D 36 ASN cc_start: 0.9309 (m-40) cc_final: 0.9036 (m110) REVERT: D 95 ARG cc_start: 0.5663 (OUTLIER) cc_final: 0.2830 (ptt180) REVERT: D 102 GLU cc_start: 0.8241 (tt0) cc_final: 0.7986 (mp0) REVERT: D 127 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8634 (t80) REVERT: D 135 ARG cc_start: 0.8930 (ttt180) cc_final: 0.8557 (tpt170) REVERT: D 139 ASP cc_start: 0.8516 (m-30) cc_final: 0.8284 (m-30) REVERT: D 201 MET cc_start: 0.4228 (ttt) cc_final: 0.0784 (mmt) REVERT: D 327 LEU cc_start: 0.9493 (mt) cc_final: 0.9217 (mp) REVERT: D 333 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: D 334 THR cc_start: 0.9160 (m) cc_final: 0.8550 (m) REVERT: D 362 LEU cc_start: 0.9695 (mt) cc_final: 0.9440 (tp) REVERT: D 481 ILE cc_start: 0.9263 (mt) cc_final: 0.8719 (mm) REVERT: M 112 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7469 (mp) REVERT: M 186 MET cc_start: 0.8514 (tmm) cc_final: 0.8287 (tpp) REVERT: M 271 ARG cc_start: 0.9214 (mtt180) cc_final: 0.8860 (mmm160) REVERT: N 110 TYR cc_start: 0.9167 (m-80) cc_final: 0.8908 (m-80) REVERT: N 170 TYR cc_start: 0.8792 (m-80) cc_final: 0.8524 (m-80) REVERT: N 222 LEU cc_start: 0.1566 (OUTLIER) cc_final: 0.0957 (tp) REVERT: N 269 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7090 (mt) REVERT: N 276 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6150 (m-80) REVERT: N 292 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6490 (tpm170) REVERT: O 108 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7612 (mm) REVERT: O 169 THR cc_start: 0.2927 (OUTLIER) cc_final: 0.2625 (m) REVERT: O 179 TRP cc_start: 0.1504 (t-100) cc_final: 0.0865 (t-100) REVERT: O 256 THR cc_start: 0.1125 (t) cc_final: 0.0321 (m) REVERT: O 296 MET cc_start: 0.4710 (mtt) cc_final: 0.4158 (pmm) REVERT: P 97 LEU cc_start: -0.1502 (OUTLIER) cc_final: -0.2282 (tt) REVERT: P 147 LEU cc_start: 0.4542 (tp) cc_final: 0.4072 (tp) REVERT: P 186 MET cc_start: 0.6764 (tmm) cc_final: 0.6181 (mtt) REVERT: P 205 SER cc_start: 0.1948 (p) cc_final: 0.1608 (p) REVERT: P 244 LEU cc_start: -0.3718 (mt) cc_final: -0.4108 (mp) REVERT: Q 15 LYS cc_start: 0.9461 (tttt) cc_final: 0.9240 (tppt) REVERT: Q 188 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8857 (p0) REVERT: Q 209 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8563 (pp) REVERT: Q 277 LYS cc_start: 0.9058 (mttt) cc_final: 0.8797 (mppt) REVERT: Q 282 MET cc_start: 0.8748 (mmm) cc_final: 0.8378 (tpp) REVERT: Q 297 LEU cc_start: 0.9320 (tp) cc_final: 0.9107 (mm) REVERT: h 282 MET cc_start: 0.8510 (tmt) cc_final: 0.8118 (mtp) REVERT: i 30 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6711 (p-80) REVERT: i 183 GLN cc_start: 0.8629 (mt0) cc_final: 0.8404 (mm110) REVERT: i 186 MET cc_start: 0.8600 (ttm) cc_final: 0.8396 (mmm) REVERT: i 202 TYR cc_start: 0.9497 (t80) cc_final: 0.9200 (t80) REVERT: i 204 MET cc_start: 0.7597 (tpt) cc_final: 0.7157 (mtt) REVERT: i 256 THR cc_start: 0.8251 (m) cc_final: 0.7490 (p) REVERT: i 299 VAL cc_start: 0.7053 (OUTLIER) cc_final: 0.6754 (m) REVERT: j 179 TRP cc_start: 0.6013 (t-100) cc_final: 0.5525 (t-100) REVERT: j 217 VAL cc_start: 0.4066 (m) cc_final: 0.3847 (t) REVERT: k 186 MET cc_start: 0.5725 (ttm) cc_final: 0.5412 (mmt) REVERT: k 204 MET cc_start: -0.2240 (tpt) cc_final: -0.2779 (mtt) REVERT: k 300 SER cc_start: 0.3697 (p) cc_final: 0.3169 (t) REVERT: l 119 LYS cc_start: 0.9340 (mttt) cc_final: 0.9064 (mppt) REVERT: l 204 MET cc_start: 0.8901 (tpt) cc_final: 0.8459 (ttp) outliers start: 210 outliers final: 71 residues processed: 880 average time/residue: 0.2458 time to fit residues: 346.6842 Evaluate side-chains 473 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 380 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [432, 197, 388, 455, 215, 20, 132, 494, 261, 248, 207] chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 0.0020 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AJ 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 212 ASN AJ 246 ASN AY 200 HIS Ah 81 GLN Ah 153 HIS Ah 232 GLN Ah 265 GLN Ah 334 GLN Ah 443 HIS Ah 562 GLN Ao 83 HIS ** Ao 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 83 HIS ** Ap 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN M 132 ASN M 176 GLN M 278 ASN N 160 HIS N 278 ASN O 176 GLN Q 241 ASN ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 102 HIS h 200 HIS ** h 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 315 ASN i 102 HIS ** i 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 176 GLN i 315 ASN j 231 ASN j 274 GLN j 315 ASN k 160 HIS k 176 GLN k 200 HIS k 315 ASN l 176 GLN ** l 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 231 ASN ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.093637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067097 restraints weight = 309275.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.066146 restraints weight = 178603.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066278 restraints weight = 118357.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066350 restraints weight = 78178.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066748 restraints weight = 61500.146| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.108 41134 Z= 0.412 Angle : 0.669 20.557 55935 Z= 0.354 Chirality : 0.041 0.335 6352 Planarity : 0.005 0.114 7175 Dihedral : 4.437 50.611 5597 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.74 % Favored : 92.08 % Rotamer: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4976 helix: 2.00 (0.11), residues: 2266 sheet: -1.14 (0.24), residues: 488 loop : -2.16 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG j 271 TYR 0.057 0.002 TYR D 89 PHE 0.024 0.002 PHE i 23 TRP 0.024 0.001 TRP O 116 HIS 0.037 0.002 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01002 / 0.41 (41132) covalent geometry : angle 0.66849 / 0.35 (55931) SS BOND : bond 0.00627 / 0.31 ( 2) SS BOND : angle 2.51409 / 1.41 ( 4) hydrogen bonds : bond 0.04507 / 3.03 ( 1761) hydrogen bonds : angle 4.87865 / 3.45 ( 5088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 466 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9745 (tttt) cc_final: 0.9163 (pptt) REVERT: AJ 113 ASP cc_start: 0.8618 (t0) cc_final: 0.7557 (t0) REVERT: AJ 139 GLN cc_start: 0.9560 (tt0) cc_final: 0.9225 (tm-30) REVERT: AJ 176 MET cc_start: 0.9340 (mpp) cc_final: 0.8982 (mpp) REVERT: AY 44 ASN cc_start: 0.8295 (p0) cc_final: 0.8065 (p0) REVERT: AY 198 MET cc_start: 0.9463 (mtt) cc_final: 0.8879 (mpp) REVERT: Ah 461 MET cc_start: 0.8627 (tmm) cc_final: 0.8253 (tmm) REVERT: Ah 537 MET cc_start: 0.9066 (ttm) cc_final: 0.8456 (mmm) REVERT: Ah 618 LEU cc_start: 0.9237 (tt) cc_final: 0.8405 (tt) REVERT: Ao 128 LEU cc_start: 0.9321 (mm) cc_final: 0.9076 (tt) REVERT: Ao 202 ASP cc_start: 0.9393 (m-30) cc_final: 0.9112 (t0) REVERT: Ao 206 ARG cc_start: 0.9334 (mtt-85) cc_final: 0.9077 (mtt180) REVERT: Ao 406 LYS cc_start: 0.9603 (ptpt) cc_final: 0.9319 (pttm) REVERT: Ao 407 GLN cc_start: 0.9333 (tt0) cc_final: 0.8864 (pt0) REVERT: Ap 131 ARG cc_start: 0.8981 (ptp-110) cc_final: 0.8674 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8603 (m90) cc_final: 0.8254 (m90) REVERT: Ap 390 MET cc_start: 0.9555 (mtp) cc_final: 0.9101 (mtm) REVERT: Ap 394 MET cc_start: 0.9558 (ttp) cc_final: 0.8957 (mmp) REVERT: Ap 405 LEU cc_start: 0.9682 (tt) cc_final: 0.9453 (pp) REVERT: Ap 406 LYS cc_start: 0.9678 (ttmm) cc_final: 0.9317 (tppp) REVERT: D 1 MET cc_start: 0.0780 (mtt) cc_final: 0.0327 (mtt) REVERT: D 4 LEU cc_start: 0.9420 (tt) cc_final: 0.9209 (tt) REVERT: D 37 ARG cc_start: 0.9150 (mtt180) cc_final: 0.8868 (ptp-110) REVERT: D 134 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 135 ARG cc_start: 0.8886 (ttt180) cc_final: 0.8565 (tpt170) REVERT: D 139 ASP cc_start: 0.8667 (m-30) cc_final: 0.8319 (m-30) REVERT: D 201 MET cc_start: 0.4401 (ttt) cc_final: 0.0882 (mmt) REVERT: D 254 ASP cc_start: 0.9375 (m-30) cc_final: 0.9091 (m-30) REVERT: D 327 LEU cc_start: 0.9457 (mt) cc_final: 0.9226 (mp) REVERT: D 362 LEU cc_start: 0.9700 (mt) cc_final: 0.9437 (tp) REVERT: D 481 ILE cc_start: 0.9296 (mt) cc_final: 0.8819 (mm) REVERT: M 20 ARG cc_start: 0.8594 (ptp90) cc_final: 0.8347 (tpt90) REVERT: M 116 TRP cc_start: 0.8934 (t60) cc_final: 0.8716 (t60) REVERT: M 186 MET cc_start: 0.8493 (tmm) cc_final: 0.8243 (tpp) REVERT: N 170 TYR cc_start: 0.8482 (m-80) cc_final: 0.8216 (m-80) REVERT: N 292 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6576 (tpm170) REVERT: O 179 TRP cc_start: 0.1254 (t-100) cc_final: 0.0861 (t-100) REVERT: P 186 MET cc_start: 0.6886 (tmm) cc_final: 0.6282 (mtt) REVERT: Q 15 LYS cc_start: 0.9414 (tttt) cc_final: 0.9208 (tppt) REVERT: Q 297 LEU cc_start: 0.9209 (tp) cc_final: 0.8896 (mm) REVERT: i 30 HIS cc_start: 0.7354 (m90) cc_final: 0.6934 (p-80) REVERT: i 202 TYR cc_start: 0.9225 (t80) cc_final: 0.8876 (t80) REVERT: j 110 TYR cc_start: 0.9169 (m-10) cc_final: 0.8785 (t80) REVERT: j 162 PHE cc_start: 0.0968 (m-10) cc_final: 0.0656 (m-10) REVERT: j 186 MET cc_start: 0.8612 (ttp) cc_final: 0.8343 (tpp) REVERT: k 204 MET cc_start: -0.2411 (tpt) cc_final: -0.2910 (mtt) REVERT: k 282 MET cc_start: 0.2340 (tpp) cc_final: 0.1902 (tpp) REVERT: k 300 SER cc_start: 0.3608 (p) cc_final: 0.3358 (t) REVERT: l 119 LYS cc_start: 0.9235 (mttt) cc_final: 0.8644 (mppt) REVERT: l 122 GLU cc_start: 0.9118 (pt0) cc_final: 0.8772 (pp20) REVERT: l 204 MET cc_start: 0.8865 (tpt) cc_final: 0.8361 (ttp) REVERT: l 256 THR cc_start: 0.9020 (m) cc_final: 0.8777 (m) outliers start: 11 outliers final: 2 residues processed: 474 average time/residue: 0.2476 time to fit residues: 188.2452 Evaluate side-chains 332 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [129, 434, 200, 231, 329, 326, 6, 366, 174, 485, 149] chunk 129 optimal weight: 0.8980 chunk 434 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 366 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 485 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AJ 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 81 GLN Ah 334 GLN Ah 638 HIS Ao 224 ASN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 224 ASN ** M 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 GLN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 HIS Q 241 ASN ** h 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 HIS ** i 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 231 ASN j 231 ASN l 188 ASN ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.093205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.066429 restraints weight = 311708.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065278 restraints weight = 173927.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065826 restraints weight = 113823.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066042 restraints weight = 78187.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066152 restraints weight = 61694.833| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.194 41134 Z= 0.397 Angle : 0.619 19.605 55935 Z= 0.327 Chirality : 0.040 0.293 6352 Planarity : 0.005 0.113 7175 Dihedral : 4.436 49.112 5597 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.50 % Favored : 92.32 % Rotamer: Outliers : 0.19 % Allowed : 3.39 % Favored : 96.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 4976 helix: 1.82 (0.11), residues: 2279 sheet: -1.42 (0.22), residues: 535 loop : -2.17 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 292 TYR 0.055 0.002 TYR D 89 PHE 0.030 0.002 PHE M 260 TRP 0.022 0.001 TRP j 179 HIS 0.036 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00984 / 0.40 (41132) covalent geometry : angle 0.61764 / 0.33 (55931) SS BOND : bond 0.00756 / 0.37 ( 2) SS BOND : angle 3.99755 / 2.26 ( 4) hydrogen bonds : bond 0.03970 / 2.67 ( 1761) hydrogen bonds : angle 4.70318 / 3.32 ( 5088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 421 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 59 ARG cc_start: 0.9163 (ttm170) cc_final: 0.8962 (mtp85) REVERT: AJ 75 LYS cc_start: 0.9736 (tttt) cc_final: 0.9189 (pptt) REVERT: AJ 113 ASP cc_start: 0.8534 (t0) cc_final: 0.7644 (t0) REVERT: AJ 138 GLU cc_start: 0.9179 (pp20) cc_final: 0.8771 (pp20) REVERT: AJ 139 GLN cc_start: 0.9531 (tt0) cc_final: 0.9287 (tm-30) REVERT: AJ 176 MET cc_start: 0.9324 (mpp) cc_final: 0.9033 (mpp) REVERT: AJ 223 GLN cc_start: 0.9135 (tt0) cc_final: 0.8605 (tt0) REVERT: AY 10 GLU cc_start: 0.7156 (tt0) cc_final: 0.6129 (tm-30) REVERT: AY 44 ASN cc_start: 0.8325 (p0) cc_final: 0.8110 (p0) REVERT: AY 198 MET cc_start: 0.9427 (mtt) cc_final: 0.8830 (mpp) REVERT: Ah 64 MET cc_start: 0.8687 (ptt) cc_final: 0.8462 (ptt) REVERT: Ah 296 MET cc_start: 0.8780 (mmp) cc_final: 0.8539 (mmp) REVERT: Ah 299 MET cc_start: 0.8192 (mpp) cc_final: 0.7702 (mmp) REVERT: Ah 461 MET cc_start: 0.8662 (tmm) cc_final: 0.8244 (tmm) REVERT: Ah 617 THR cc_start: 0.9324 (m) cc_final: 0.9007 (p) REVERT: Ah 621 LYS cc_start: 0.9490 (ptpp) cc_final: 0.8839 (pttt) REVERT: Ao 128 LEU cc_start: 0.9341 (mm) cc_final: 0.9082 (tt) REVERT: Ao 155 ILE cc_start: 0.8939 (pt) cc_final: 0.8651 (pt) REVERT: Ao 202 ASP cc_start: 0.9384 (m-30) cc_final: 0.9043 (t0) REVERT: Ao 206 ARG cc_start: 0.9303 (mtt-85) cc_final: 0.8988 (mmm160) REVERT: Ao 393 ASP cc_start: 0.9007 (t0) cc_final: 0.8745 (t0) REVERT: Ao 406 LYS cc_start: 0.9631 (ptpt) cc_final: 0.9305 (pttm) REVERT: Ao 407 GLN cc_start: 0.9235 (tt0) cc_final: 0.8766 (pt0) REVERT: Ao 408 MET cc_start: 0.9227 (mtm) cc_final: 0.9018 (mtp) REVERT: Ap 131 ARG cc_start: 0.8953 (ptp-110) cc_final: 0.8606 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8674 (m90) cc_final: 0.8310 (m90) REVERT: Ap 305 TYR cc_start: 0.8924 (m-80) cc_final: 0.8362 (m-80) REVERT: Ap 390 MET cc_start: 0.9533 (mtp) cc_final: 0.9191 (mtp) REVERT: Ap 394 MET cc_start: 0.9531 (ttp) cc_final: 0.8890 (mmp) REVERT: Ap 405 LEU cc_start: 0.9696 (tt) cc_final: 0.9415 (pp) REVERT: Ap 422 TYR cc_start: 0.9223 (m-80) cc_final: 0.8776 (m-80) REVERT: D 1 MET cc_start: 0.0755 (mtt) cc_final: 0.0333 (mtt) REVERT: D 135 ARG cc_start: 0.8884 (ttt180) cc_final: 0.8547 (tpt170) REVERT: D 139 ASP cc_start: 0.8674 (m-30) cc_final: 0.8342 (m-30) REVERT: D 201 MET cc_start: 0.4446 (ttt) cc_final: 0.0924 (mmt) REVERT: D 212 LYS cc_start: 0.8065 (ptpp) cc_final: 0.7727 (ptpt) REVERT: D 254 ASP cc_start: 0.9374 (m-30) cc_final: 0.9082 (m-30) REVERT: D 481 ILE cc_start: 0.9315 (mt) cc_final: 0.8836 (mm) REVERT: M 20 ARG cc_start: 0.8811 (ptp90) cc_final: 0.8467 (tpt90) REVERT: M 110 TYR cc_start: 0.9289 (m-80) cc_final: 0.8974 (m-80) REVERT: M 186 MET cc_start: 0.8570 (tmm) cc_final: 0.8337 (tpp) REVERT: M 296 MET cc_start: 0.8731 (mtt) cc_final: 0.8441 (mtt) REVERT: N 110 TYR cc_start: 0.9414 (m-80) cc_final: 0.9155 (m-80) REVERT: N 292 ARG cc_start: 0.8067 (mtt180) cc_final: 0.6464 (tpm170) REVERT: P 21 ILE cc_start: 0.5113 (tp) cc_final: 0.4871 (tp) REVERT: P 186 MET cc_start: 0.6880 (tmm) cc_final: 0.6284 (mtt) REVERT: Q 15 LYS cc_start: 0.9441 (tttt) cc_final: 0.9221 (tppt) REVERT: h 282 MET cc_start: 0.7907 (tmm) cc_final: 0.7481 (mtp) REVERT: i 30 HIS cc_start: 0.7329 (m90) cc_final: 0.6958 (p-80) REVERT: i 186 MET cc_start: 0.7703 (mmm) cc_final: 0.7394 (mmm) REVERT: j 110 TYR cc_start: 0.9097 (m-10) cc_final: 0.8737 (t80) REVERT: k 204 MET cc_start: -0.2365 (tpt) cc_final: -0.2865 (mtt) REVERT: k 300 SER cc_start: 0.3594 (p) cc_final: 0.3371 (t) REVERT: l 119 LYS cc_start: 0.9242 (mttt) cc_final: 0.8608 (mppt) REVERT: l 122 GLU cc_start: 0.9193 (pt0) cc_final: 0.8800 (pp20) REVERT: l 204 MET cc_start: 0.8874 (tpt) cc_final: 0.8329 (ttp) REVERT: l 256 THR cc_start: 0.9043 (m) cc_final: 0.8628 (m) outliers start: 8 outliers final: 0 residues processed: 422 average time/residue: 0.2564 time to fit residues: 173.2120 Evaluate side-chains 331 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [12, 289, 82, 385, 207, 455, 392, 44, 308, 34, 260] chunk 12 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 455 optimal weight: 20.0000 chunk 392 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 260 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ah 334 GLN Ao 212 HIS ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 214 GLN M 278 ASN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 241 ASN ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 238 ASN i 102 HIS ** i 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 231 ASN ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.092178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066095 restraints weight = 309980.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.064869 restraints weight = 180669.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064947 restraints weight = 118396.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065190 restraints weight = 86744.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065485 restraints weight = 63220.248| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.302 41134 Z= 0.410 Angle : 0.649 18.541 55935 Z= 0.340 Chirality : 0.040 0.319 6352 Planarity : 0.005 0.111 7175 Dihedral : 4.569 47.316 5597 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.98 % Favored : 91.86 % Rotamer: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 4976 helix: 1.71 (0.11), residues: 2278 sheet: -1.42 (0.23), residues: 520 loop : -2.28 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 152 TYR 0.046 0.002 TYR D 89 PHE 0.029 0.002 PHE l 260 TRP 0.021 0.001 TRP O 116 HIS 0.030 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01016 / 0.41 (41132) covalent geometry : angle 0.64679 / 0.34 (55931) SS BOND : bond 0.01580 / 0.76 ( 2) SS BOND : angle 5.94358 / 3.35 ( 4) hydrogen bonds : bond 0.03808 / 2.57 ( 1761) hydrogen bonds : angle 4.73369 / 3.34 ( 5088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 393 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 59 ARG cc_start: 0.9230 (ttm170) cc_final: 0.8972 (mtp85) REVERT: AJ 73 TYR cc_start: 0.9500 (t80) cc_final: 0.7070 (m-10) REVERT: AJ 75 LYS cc_start: 0.9777 (tttt) cc_final: 0.9230 (pttt) REVERT: AJ 77 LEU cc_start: 0.9700 (mp) cc_final: 0.9351 (mt) REVERT: AJ 95 GLU cc_start: 0.9043 (pm20) cc_final: 0.8795 (pm20) REVERT: AJ 113 ASP cc_start: 0.8599 (t0) cc_final: 0.7538 (t0) REVERT: AJ 138 GLU cc_start: 0.9246 (pp20) cc_final: 0.8841 (pp20) REVERT: AJ 139 GLN cc_start: 0.9547 (tt0) cc_final: 0.9284 (tm-30) REVERT: AJ 223 GLN cc_start: 0.9084 (tt0) cc_final: 0.8515 (tt0) REVERT: AY 10 GLU cc_start: 0.7215 (tt0) cc_final: 0.6207 (tm-30) REVERT: AY 44 ASN cc_start: 0.8430 (p0) cc_final: 0.8157 (p0) REVERT: Ah 64 MET cc_start: 0.8726 (ptt) cc_final: 0.8487 (ptt) REVERT: Ah 398 MET cc_start: 0.8007 (mtm) cc_final: 0.7536 (mtm) REVERT: Ah 461 MET cc_start: 0.8720 (tmm) cc_final: 0.8333 (tmm) REVERT: Ah 537 MET cc_start: 0.8707 (tpp) cc_final: 0.8434 (tpp) REVERT: Ah 618 LEU cc_start: 0.9571 (tt) cc_final: 0.9131 (mp) REVERT: Ah 621 LYS cc_start: 0.9453 (ptpp) cc_final: 0.8899 (pttt) REVERT: Ao 155 ILE cc_start: 0.9071 (pt) cc_final: 0.8869 (pt) REVERT: Ao 202 ASP cc_start: 0.9391 (m-30) cc_final: 0.9039 (t0) REVERT: Ao 206 ARG cc_start: 0.9359 (mtt-85) cc_final: 0.8909 (mtt180) REVERT: Ao 393 ASP cc_start: 0.9093 (t0) cc_final: 0.8786 (t0) REVERT: Ao 406 LYS cc_start: 0.9649 (ptpt) cc_final: 0.9324 (pttm) REVERT: Ao 407 GLN cc_start: 0.9284 (tt0) cc_final: 0.8563 (pt0) REVERT: Ao 408 MET cc_start: 0.9331 (mtm) cc_final: 0.9043 (mtp) REVERT: Ap 131 ARG cc_start: 0.8834 (ptp-110) cc_final: 0.8507 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8781 (m90) cc_final: 0.8364 (m90) REVERT: Ap 305 TYR cc_start: 0.8862 (m-80) cc_final: 0.8218 (m-80) REVERT: Ap 390 MET cc_start: 0.9538 (mtp) cc_final: 0.9028 (mtm) REVERT: Ap 394 MET cc_start: 0.9424 (ttp) cc_final: 0.8818 (mmp) REVERT: D 1 MET cc_start: 0.1012 (mtt) cc_final: 0.0544 (mtt) REVERT: D 134 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8286 (mt-10) REVERT: D 135 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8573 (tpt170) REVERT: D 139 ASP cc_start: 0.8775 (m-30) cc_final: 0.8307 (m-30) REVERT: D 201 MET cc_start: 0.4339 (ttt) cc_final: 0.1273 (mmt) REVERT: D 212 LYS cc_start: 0.8135 (ptpp) cc_final: 0.7799 (ptpt) REVERT: D 254 ASP cc_start: 0.9347 (m-30) cc_final: 0.9068 (m-30) REVERT: D 481 ILE cc_start: 0.9324 (mt) cc_final: 0.8878 (mm) REVERT: M 110 TYR cc_start: 0.9231 (m-80) cc_final: 0.8863 (m-80) REVERT: N 110 TYR cc_start: 0.9431 (m-80) cc_final: 0.9168 (m-80) REVERT: N 292 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6523 (tpm170) REVERT: O 296 MET cc_start: 0.6499 (ttm) cc_final: 0.6001 (pmm) REVERT: P 21 ILE cc_start: 0.5177 (tp) cc_final: 0.4927 (tp) REVERT: P 186 MET cc_start: 0.6221 (tmm) cc_final: 0.5553 (mtt) REVERT: Q 15 LYS cc_start: 0.9480 (tttt) cc_final: 0.9231 (tppt) REVERT: h 282 MET cc_start: 0.7651 (tmm) cc_final: 0.7214 (mtp) REVERT: i 30 HIS cc_start: 0.7375 (m90) cc_final: 0.6938 (p-80) REVERT: i 186 MET cc_start: 0.7779 (mmm) cc_final: 0.7439 (mmm) REVERT: j 110 TYR cc_start: 0.9173 (m-10) cc_final: 0.8792 (t80) REVERT: j 162 PHE cc_start: 0.0555 (m-10) cc_final: 0.0332 (m-80) REVERT: k 204 MET cc_start: -0.2764 (tpt) cc_final: -0.3219 (mtt) REVERT: k 300 SER cc_start: 0.4323 (p) cc_final: 0.4055 (t) REVERT: l 119 LYS cc_start: 0.9235 (mttt) cc_final: 0.8562 (mppt) REVERT: l 122 GLU cc_start: 0.9380 (pt0) cc_final: 0.8820 (pp20) REVERT: l 204 MET cc_start: 0.8797 (tpt) cc_final: 0.8017 (ppp) outliers start: 3 outliers final: 1 residues processed: 395 average time/residue: 0.2431 time to fit residues: 155.0061 Evaluate side-chains 311 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [360, 193, 228, 489, 10, 403, 266, 352, 272, 189, 181] chunk 360 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 489 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 403 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 272 optimal weight: 0.0270 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AJ 200 HIS Ah 300 HIS Ah 334 GLN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 ASN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN Q 241 ASN ** h 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 HIS ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.094259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067335 restraints weight = 303245.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065671 restraints weight = 163907.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066056 restraints weight = 105909.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066250 restraints weight = 77139.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.066407 restraints weight = 61478.162| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.180 41134 Z= 0.380 Angle : 0.572 19.387 55935 Z= 0.300 Chirality : 0.039 0.257 6352 Planarity : 0.004 0.105 7175 Dihedral : 4.310 46.199 5597 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.07 % Rotamer: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.12), residues: 4976 helix: 1.93 (0.11), residues: 2284 sheet: -1.30 (0.23), residues: 528 loop : -2.16 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 292 TYR 0.060 0.001 TYR D 89 PHE 0.028 0.001 PHE M 260 TRP 0.029 0.001 TRPAo 248 HIS 0.038 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00946 / 0.38 (41132) covalent geometry : angle 0.57197 / 0.30 (55931) SS BOND : bond 0.01501 / 0.72 ( 2) SS BOND : angle 2.63970 / 1.34 ( 4) hydrogen bonds : bond 0.03304 / 2.22 ( 1761) hydrogen bonds : angle 4.37699 / 3.09 ( 5088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 415 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9715 (tttt) cc_final: 0.9185 (pptt) REVERT: AJ 113 ASP cc_start: 0.8778 (t0) cc_final: 0.8019 (t0) REVERT: AJ 138 GLU cc_start: 0.9187 (pp20) cc_final: 0.8716 (pp20) REVERT: AJ 139 GLN cc_start: 0.9586 (tt0) cc_final: 0.9380 (tm-30) REVERT: AJ 176 MET cc_start: 0.9343 (mpp) cc_final: 0.9038 (mpp) REVERT: AJ 198 MET cc_start: 0.8713 (mmp) cc_final: 0.8476 (mmm) REVERT: AJ 223 GLN cc_start: 0.9164 (tt0) cc_final: 0.8808 (tt0) REVERT: AY 10 GLU cc_start: 0.7082 (tt0) cc_final: 0.6847 (tp30) REVERT: AY 44 ASN cc_start: 0.8318 (p0) cc_final: 0.8099 (p0) REVERT: Ah 64 MET cc_start: 0.8302 (ptt) cc_final: 0.8003 (ptt) REVERT: Ah 405 MET cc_start: 0.8891 (ppp) cc_final: 0.8478 (ppp) REVERT: Ah 461 MET cc_start: 0.8666 (tmm) cc_final: 0.8238 (tmm) REVERT: Ah 537 MET cc_start: 0.8880 (tpp) cc_final: 0.8450 (tpp) REVERT: Ah 617 THR cc_start: 0.9317 (m) cc_final: 0.8928 (p) REVERT: Ah 618 LEU cc_start: 0.9513 (tt) cc_final: 0.9045 (mp) REVERT: Ah 621 LYS cc_start: 0.9473 (ptpp) cc_final: 0.8748 (pttt) REVERT: Ao 155 ILE cc_start: 0.8857 (pt) cc_final: 0.8501 (pt) REVERT: Ao 393 ASP cc_start: 0.8966 (t0) cc_final: 0.8674 (t0) REVERT: Ao 406 LYS cc_start: 0.9616 (ptpt) cc_final: 0.9156 (pttm) REVERT: Ao 407 GLN cc_start: 0.9321 (tt0) cc_final: 0.8821 (pt0) REVERT: Ap 131 ARG cc_start: 0.8950 (ptp-110) cc_final: 0.8479 (ptp-170) REVERT: Ap 394 MET cc_start: 0.9500 (ttp) cc_final: 0.8743 (mmp) REVERT: Ap 405 LEU cc_start: 0.9694 (tt) cc_final: 0.9444 (pp) REVERT: Ap 422 TYR cc_start: 0.9255 (m-80) cc_final: 0.8841 (m-80) REVERT: D 1 MET cc_start: 0.0924 (mtt) cc_final: -0.0049 (mtt) REVERT: D 36 ASN cc_start: 0.9069 (m-40) cc_final: 0.8769 (m110) REVERT: D 79 ASN cc_start: 0.9348 (t0) cc_final: 0.9072 (t0) REVERT: D 134 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 135 ARG cc_start: 0.8828 (ttt180) cc_final: 0.8499 (tpt170) REVERT: D 139 ASP cc_start: 0.8568 (m-30) cc_final: 0.8278 (m-30) REVERT: D 201 MET cc_start: 0.4291 (ttt) cc_final: 0.2272 (mmt) REVERT: D 212 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7715 (ptpt) REVERT: D 254 ASP cc_start: 0.9236 (m-30) cc_final: 0.9014 (m-30) REVERT: D 481 ILE cc_start: 0.9224 (mt) cc_final: 0.8745 (mm) REVERT: M 110 TYR cc_start: 0.9111 (m-80) cc_final: 0.8804 (m-80) REVERT: N 110 TYR cc_start: 0.9357 (m-80) cc_final: 0.9138 (m-80) REVERT: N 292 ARG cc_start: 0.7765 (mtt180) cc_final: 0.6627 (tpm170) REVERT: O 296 MET cc_start: 0.6928 (ttm) cc_final: 0.6470 (pmm) REVERT: P 21 ILE cc_start: 0.5559 (tp) cc_final: 0.5352 (tp) REVERT: P 186 MET cc_start: 0.6139 (tmm) cc_final: 0.5486 (mtt) REVERT: Q 15 LYS cc_start: 0.9475 (tttt) cc_final: 0.9214 (tppt) REVERT: Q 260 PHE cc_start: 0.8053 (m-10) cc_final: 0.7827 (m-10) REVERT: h 204 MET cc_start: 0.8079 (ppp) cc_final: 0.6920 (ppp) REVERT: h 296 MET cc_start: 0.8363 (pmm) cc_final: 0.7412 (pmm) REVERT: i 30 HIS cc_start: 0.7300 (m90) cc_final: 0.6846 (p-80) REVERT: i 186 MET cc_start: 0.7765 (mmm) cc_final: 0.7427 (mmm) REVERT: j 110 TYR cc_start: 0.9201 (m-10) cc_final: 0.8797 (t80) REVERT: k 204 MET cc_start: -0.2826 (tpt) cc_final: -0.3301 (mtt) REVERT: k 300 SER cc_start: 0.4319 (p) cc_final: 0.4014 (t) REVERT: l 186 MET cc_start: 0.8407 (ttt) cc_final: 0.7360 (tmm) REVERT: l 204 MET cc_start: 0.8771 (tpt) cc_final: 0.7943 (ppp) outliers start: 3 outliers final: 1 residues processed: 416 average time/residue: 0.2391 time to fit residues: 161.1904 Evaluate side-chains 320 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [396, 302, 476, 234, 457, 163, 69, 380, 122, 359, 323] chunk 396 optimal weight: 20.0000 chunk 302 optimal weight: 20.0000 chunk 476 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 457 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 380 optimal weight: 8.9990 chunk 122 optimal weight: 0.2980 chunk 359 optimal weight: 8.9990 chunk 323 optimal weight: 3.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ah 334 GLN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 278 ASN O 188 ASN ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 188 ASN l 176 GLN ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.091277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064925 restraints weight = 318604.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063120 restraints weight = 182741.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.063299 restraints weight = 120444.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063559 restraints weight = 85456.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.063583 restraints weight = 68156.596| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.248 41134 Z= 0.417 Angle : 0.657 18.662 55935 Z= 0.345 Chirality : 0.040 0.267 6352 Planarity : 0.005 0.121 7175 Dihedral : 4.566 54.346 5597 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.20 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4976 helix: 1.73 (0.11), residues: 2283 sheet: -1.22 (0.24), residues: 490 loop : -2.29 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 20 TYR 0.051 0.002 TYR D 89 PHE 0.026 0.002 PHE O 234 TRP 0.030 0.001 TRPAo 248 HIS 0.036 0.002 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01020 / 0.42 (41132) covalent geometry : angle 0.65546 / 0.34 (55931) SS BOND : bond 0.01043 / 0.51 ( 2) SS BOND : angle 4.48275 / 2.44 ( 4) hydrogen bonds : bond 0.03702 / 2.49 ( 1761) hydrogen bonds : angle 4.67039 / 3.29 ( 5088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9741 (tttt) cc_final: 0.9285 (pttt) REVERT: AJ 198 MET cc_start: 0.8720 (mmp) cc_final: 0.8501 (mmp) REVERT: AY 10 GLU cc_start: 0.7196 (tt0) cc_final: 0.6515 (tm-30) REVERT: AY 44 ASN cc_start: 0.8397 (p0) cc_final: 0.8147 (p0) REVERT: AY 176 MET cc_start: 0.7495 (mtp) cc_final: 0.6911 (mtp) REVERT: Ah 335 MET cc_start: 0.8572 (pmm) cc_final: 0.7953 (ptp) REVERT: Ah 398 MET cc_start: 0.8018 (mtm) cc_final: 0.7649 (mtm) REVERT: Ah 405 MET cc_start: 0.8938 (ppp) cc_final: 0.8466 (ppp) REVERT: Ah 461 MET cc_start: 0.8498 (tmm) cc_final: 0.8224 (tmm) REVERT: Ah 537 MET cc_start: 0.8882 (tpp) cc_final: 0.8497 (tpp) REVERT: Ah 618 LEU cc_start: 0.9505 (tt) cc_final: 0.9031 (mp) REVERT: Ah 621 LYS cc_start: 0.9475 (ptpp) cc_final: 0.9035 (pttt) REVERT: Ah 623 MET cc_start: 0.8152 (tpp) cc_final: 0.7676 (tpt) REVERT: Ao 202 ASP cc_start: 0.9356 (m-30) cc_final: 0.8948 (t0) REVERT: Ao 244 PHE cc_start: 0.9382 (t80) cc_final: 0.9117 (t80) REVERT: Ao 384 MET cc_start: 0.7672 (tpp) cc_final: 0.7250 (tpp) REVERT: Ao 393 ASP cc_start: 0.8937 (t0) cc_final: 0.8649 (t0) REVERT: Ao 406 LYS cc_start: 0.9594 (ptpt) cc_final: 0.9207 (pttm) REVERT: Ao 407 GLN cc_start: 0.9332 (tt0) cc_final: 0.8635 (pt0) REVERT: Ap 131 ARG cc_start: 0.8817 (ptp-110) cc_final: 0.8507 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8467 (m-70) cc_final: 0.8004 (m90) REVERT: Ap 305 TYR cc_start: 0.8927 (m-80) cc_final: 0.8364 (m-80) REVERT: Ap 394 MET cc_start: 0.9523 (ttp) cc_final: 0.8742 (mmp) REVERT: D 1 MET cc_start: 0.1567 (mtt) cc_final: 0.1051 (mtt) REVERT: D 79 ASN cc_start: 0.9244 (t0) cc_final: 0.8895 (t0) REVERT: D 135 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8541 (tpt170) REVERT: D 139 ASP cc_start: 0.8549 (m-30) cc_final: 0.8173 (m-30) REVERT: D 167 MET cc_start: 0.8385 (mmm) cc_final: 0.7976 (mmm) REVERT: D 201 MET cc_start: 0.4500 (ttt) cc_final: 0.1291 (mmt) REVERT: D 212 LYS cc_start: 0.7954 (ptpp) cc_final: 0.7615 (ptpt) REVERT: D 254 ASP cc_start: 0.9282 (m-30) cc_final: 0.9072 (m-30) REVERT: D 481 ILE cc_start: 0.9315 (mt) cc_final: 0.8920 (mm) REVERT: M 36 PHE cc_start: 0.9380 (m-10) cc_final: 0.8835 (m-80) REVERT: M 110 TYR cc_start: 0.9108 (m-80) cc_final: 0.8904 (m-80) REVERT: N 110 TYR cc_start: 0.9431 (m-80) cc_final: 0.9214 (m-80) REVERT: N 292 ARG cc_start: 0.8323 (mtt180) cc_final: 0.6502 (tpm170) REVERT: O 296 MET cc_start: 0.6515 (ttm) cc_final: 0.6041 (pmm) REVERT: P 186 MET cc_start: 0.6058 (tmm) cc_final: 0.5378 (mtt) REVERT: P 305 ASN cc_start: 0.0583 (t0) cc_final: 0.0373 (t0) REVERT: Q 15 LYS cc_start: 0.9327 (tttt) cc_final: 0.9078 (tppt) REVERT: Q 260 PHE cc_start: 0.8099 (m-10) cc_final: 0.7526 (m-80) REVERT: h 204 MET cc_start: 0.8197 (ppp) cc_final: 0.7099 (ppp) REVERT: h 296 MET cc_start: 0.8378 (pmm) cc_final: 0.7422 (pmm) REVERT: i 30 HIS cc_start: 0.7053 (m90) cc_final: 0.6726 (p-80) REVERT: i 186 MET cc_start: 0.8085 (mmm) cc_final: 0.7766 (mmm) REVERT: j 110 TYR cc_start: 0.9022 (m-10) cc_final: 0.8744 (t80) REVERT: j 183 GLN cc_start: 0.6302 (pp30) cc_final: 0.5781 (mm110) REVERT: j 186 MET cc_start: 0.6076 (tpt) cc_final: 0.5756 (tpp) REVERT: k 204 MET cc_start: -0.2808 (tpt) cc_final: -0.3278 (mtt) REVERT: k 300 SER cc_start: 0.4383 (p) cc_final: 0.4088 (t) REVERT: l 119 LYS cc_start: 0.9222 (mttt) cc_final: 0.8586 (mppt) REVERT: l 122 GLU cc_start: 0.8972 (pt0) cc_final: 0.8677 (pp20) REVERT: l 204 MET cc_start: 0.8621 (tpt) cc_final: 0.8025 (ppp) REVERT: l 249 TYR cc_start: 0.8503 (m-10) cc_final: 0.7996 (m-10) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2415 time to fit residues: 144.6538 Evaluate side-chains 300 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [89, 8, 328, 316, 331, 85, 381, 386, 404, 487, 415] chunk 89 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 328 optimal weight: 30.0000 chunk 316 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 381 optimal weight: 20.0000 chunk 386 optimal weight: 9.9990 chunk 404 optimal weight: 30.0000 chunk 487 optimal weight: 3.9990 chunk 415 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ah 334 GLN Ah 638 HIS ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 241 ASN k 160 HIS ** l 305 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 = 0.3847 r_free = 0.3847 target = 0.092109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065769 restraints weight = 312418.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065878 restraints weight = 182209.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065712 restraints weight = 123949.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065900 restraints weight = 83568.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066309 restraints weight = 64591.528| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.265 41134 Z= 0.394 Angle : 0.609 18.758 55935 Z= 0.320 Chirality : 0.040 0.218 6352 Planarity : 0.004 0.118 7175 Dihedral : 4.495 52.401 5597 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.34 % Favored : 92.50 % Rotamer: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.59 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 4976 helix: 1.79 (0.11), residues: 2277 sheet: -1.44 (0.22), residues: 550 loop : -2.26 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGAp 80 TYR 0.048 0.001 TYR D 89 PHE 0.040 0.001 PHE i 23 TRP 0.026 0.001 TRPAo 248 HIS 0.032 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00981 / 0.39 (41132) covalent geometry : angle 0.60805 / 0.32 (55931) SS BOND : bond 0.00490 / 0.26 ( 2) SS BOND : angle 3.76786 / 2.00 ( 4) hydrogen bonds : bond 0.03491 / 2.35 ( 1761) hydrogen bonds : angle 4.55024 / 3.21 ( 5088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9765 (tttt) cc_final: 0.9234 (pttt) REVERT: AJ 95 GLU cc_start: 0.8995 (pm20) cc_final: 0.8704 (pm20) REVERT: AJ 113 ASP cc_start: 0.8641 (t0) cc_final: 0.7818 (t0) REVERT: AJ 138 GLU cc_start: 0.9145 (pp20) cc_final: 0.8789 (pp20) REVERT: AY 10 GLU cc_start: 0.7146 (tt0) cc_final: 0.6546 (tp30) REVERT: AY 44 ASN cc_start: 0.8353 (p0) cc_final: 0.8092 (p0) REVERT: AY 176 MET cc_start: 0.7530 (mtp) cc_final: 0.6887 (mtp) REVERT: Ah 64 MET cc_start: 0.8722 (ptt) cc_final: 0.8459 (ptt) REVERT: Ah 252 MET cc_start: 0.9344 (mmp) cc_final: 0.9111 (mmp) REVERT: Ah 335 MET cc_start: 0.8563 (pmm) cc_final: 0.8091 (ptp) REVERT: Ah 398 MET cc_start: 0.8397 (mtm) cc_final: 0.7636 (mtm) REVERT: Ah 405 MET cc_start: 0.8984 (ppp) cc_final: 0.8479 (ppp) REVERT: Ah 461 MET cc_start: 0.8698 (tmm) cc_final: 0.8364 (tmm) REVERT: Ah 537 MET cc_start: 0.8876 (tpp) cc_final: 0.8460 (tpp) REVERT: Ah 618 LEU cc_start: 0.9464 (tt) cc_final: 0.9026 (mp) REVERT: Ah 621 LYS cc_start: 0.9472 (ptpp) cc_final: 0.9010 (pttt) REVERT: Ao 202 ASP cc_start: 0.9393 (m-30) cc_final: 0.9028 (t0) REVERT: Ao 384 MET cc_start: 0.7603 (tpp) cc_final: 0.7213 (tpp) REVERT: Ao 393 ASP cc_start: 0.8797 (t0) cc_final: 0.8460 (t0) REVERT: Ao 406 LYS cc_start: 0.9548 (ptpt) cc_final: 0.9177 (pttm) REVERT: Ap 131 ARG cc_start: 0.8813 (ptp-110) cc_final: 0.8474 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8588 (m-70) cc_final: 0.8044 (m90) REVERT: Ap 354 MET cc_start: 0.8335 (mmm) cc_final: 0.8133 (mmp) REVERT: Ap 390 MET cc_start: 0.9641 (mtp) cc_final: 0.9319 (mtt) REVERT: Ap 394 MET cc_start: 0.9557 (ttp) cc_final: 0.8724 (mmp) REVERT: D 1 MET cc_start: 0.1405 (mtt) cc_final: 0.0274 (mtt) REVERT: D 79 ASN cc_start: 0.9258 (t0) cc_final: 0.8946 (t0) REVERT: D 135 ARG cc_start: 0.8883 (ttt180) cc_final: 0.8383 (tpt170) REVERT: D 139 ASP cc_start: 0.8554 (m-30) cc_final: 0.8182 (m-30) REVERT: D 167 MET cc_start: 0.8484 (mmm) cc_final: 0.8042 (mmm) REVERT: D 201 MET cc_start: 0.4340 (ttt) cc_final: 0.1279 (mmt) REVERT: D 212 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7522 (ptpt) REVERT: D 462 LEU cc_start: 0.9349 (mt) cc_final: 0.8959 (tt) REVERT: D 481 ILE cc_start: 0.9304 (mt) cc_final: 0.8861 (mm) REVERT: M 36 PHE cc_start: 0.9356 (m-10) cc_final: 0.8815 (m-80) REVERT: M 110 TYR cc_start: 0.9158 (m-80) cc_final: 0.8867 (m-80) REVERT: M 186 MET cc_start: 0.8512 (ttt) cc_final: 0.8044 (tpt) REVERT: N 292 ARG cc_start: 0.8315 (mtt180) cc_final: 0.6460 (tpm170) REVERT: O 296 MET cc_start: 0.6859 (ttm) cc_final: 0.6342 (pmm) REVERT: P 186 MET cc_start: 0.6750 (tmm) cc_final: 0.5913 (mtt) REVERT: P 249 TYR cc_start: 0.6683 (m-10) cc_final: 0.6442 (m-80) REVERT: Q 15 LYS cc_start: 0.9462 (tttt) cc_final: 0.9235 (tppt) REVERT: Q 260 PHE cc_start: 0.8065 (m-10) cc_final: 0.7468 (m-80) REVERT: h 204 MET cc_start: 0.8205 (ppp) cc_final: 0.7173 (ppp) REVERT: h 296 MET cc_start: 0.8380 (pmm) cc_final: 0.7539 (pmm) REVERT: i 30 HIS cc_start: 0.6869 (m90) cc_final: 0.6331 (p-80) REVERT: i 186 MET cc_start: 0.8351 (mmm) cc_final: 0.8069 (mmm) REVERT: j 110 TYR cc_start: 0.9020 (m-10) cc_final: 0.8745 (t80) REVERT: j 183 GLN cc_start: 0.6680 (pp30) cc_final: 0.6377 (mm-40) REVERT: k 204 MET cc_start: -0.2813 (tpt) cc_final: -0.3275 (mtt) REVERT: k 300 SER cc_start: 0.4420 (p) cc_final: 0.4139 (t) REVERT: l 15 LYS cc_start: 0.9534 (mmtt) cc_final: 0.9273 (mmmm) REVERT: l 204 MET cc_start: 0.8672 (tpt) cc_final: 0.7991 (ppp) REVERT: l 249 TYR cc_start: 0.8509 (m-10) cc_final: 0.7931 (m-10) REVERT: l 256 THR cc_start: 0.8905 (m) cc_final: 0.8575 (m) outliers start: 2 outliers final: 1 residues processed: 386 average time/residue: 0.2482 time to fit residues: 157.0760 Evaluate side-chains 299 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [307, 119, 101, 13, 97, 27, 154, 64, 252, 83, 437] chunk 307 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 437 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AJ 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 231 GLN Ao 402 HIS ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 158 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 241 ASN ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 274 GLN j 200 HIS j 231 ASN ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 315 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063806 restraints weight = 315978.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062287 restraints weight = 182849.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062477 restraints weight = 123706.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062726 restraints weight = 92932.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.062789 restraints weight = 71735.936| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.322 41134 Z= 0.444 Angle : 0.739 17.766 55935 Z= 0.388 Chirality : 0.042 0.208 6352 Planarity : 0.005 0.123 7175 Dihedral : 4.967 52.562 5597 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.98 % Favored : 90.84 % Rotamer: Outliers : 0.02 % Allowed : 1.60 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.12), residues: 4976 helix: 1.31 (0.11), residues: 2281 sheet: -1.47 (0.23), residues: 479 loop : -2.50 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAh 552 TYR 0.043 0.002 TYR D 89 PHE 0.027 0.002 PHEAJ 123 TRP 0.039 0.002 TRP j 179 HIS 0.033 0.002 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01076 / 0.44 (41132) covalent geometry : angle 0.73791 / 0.39 (55931) SS BOND : bond 0.01042 / 0.52 ( 2) SS BOND : angle 5.27425 / 2.86 ( 4) hydrogen bonds : bond 0.04104 / 2.80 ( 1761) hydrogen bonds : angle 4.98311 / 3.52 ( 5088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9790 (tttt) cc_final: 0.9157 (ttpt) REVERT: AJ 138 GLU cc_start: 0.9185 (pp20) cc_final: 0.8899 (pp20) REVERT: AJ 198 MET cc_start: 0.8978 (mmp) cc_final: 0.8739 (mmp) REVERT: AY 10 GLU cc_start: 0.7389 (tt0) cc_final: 0.6689 (tp30) REVERT: AY 44 ASN cc_start: 0.8448 (p0) cc_final: 0.8199 (p0) REVERT: AY 177 LEU cc_start: 0.9405 (tp) cc_final: 0.9162 (pp) REVERT: Ah 252 MET cc_start: 0.9433 (mmp) cc_final: 0.9159 (mmm) REVERT: Ah 335 MET cc_start: 0.8580 (pmm) cc_final: 0.7988 (ptp) REVERT: Ah 398 MET cc_start: 0.8547 (mtm) cc_final: 0.7728 (mtm) REVERT: Ah 405 MET cc_start: 0.8987 (ppp) cc_final: 0.8514 (ppp) REVERT: Ah 461 MET cc_start: 0.8636 (tmm) cc_final: 0.8404 (tmm) REVERT: Ah 537 MET cc_start: 0.8913 (tpp) cc_final: 0.8563 (tpp) REVERT: Ao 202 ASP cc_start: 0.9401 (m-30) cc_final: 0.9120 (t0) REVERT: Ao 206 ARG cc_start: 0.9311 (mtt180) cc_final: 0.8954 (mmm160) REVERT: Ao 244 PHE cc_start: 0.9492 (t80) cc_final: 0.9238 (t80) REVERT: Ao 384 MET cc_start: 0.7863 (tpp) cc_final: 0.7256 (tpt) REVERT: Ao 393 ASP cc_start: 0.9023 (t0) cc_final: 0.8796 (t0) REVERT: Ap 131 ARG cc_start: 0.8924 (ptp-110) cc_final: 0.8538 (ptp-170) REVERT: Ap 212 HIS cc_start: 0.8483 (m-70) cc_final: 0.8030 (m90) REVERT: Ap 394 MET cc_start: 0.9655 (ttp) cc_final: 0.8797 (mmp) REVERT: D 1 MET cc_start: 0.1491 (mtt) cc_final: 0.1056 (mtm) REVERT: D 167 MET cc_start: 0.8508 (mmm) cc_final: 0.8084 (mmm) REVERT: D 462 LEU cc_start: 0.9428 (mt) cc_final: 0.8978 (pp) REVERT: M 36 PHE cc_start: 0.9382 (m-10) cc_final: 0.8873 (m-80) REVERT: M 110 TYR cc_start: 0.9272 (m-80) cc_final: 0.9016 (m-80) REVERT: M 126 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9016 (tm-30) REVERT: N 292 ARG cc_start: 0.8571 (mtt180) cc_final: 0.6807 (tpm170) REVERT: O 296 MET cc_start: 0.6397 (ttm) cc_final: 0.5855 (pmm) REVERT: P 186 MET cc_start: 0.6877 (tmm) cc_final: 0.6075 (mtt) REVERT: P 198 ILE cc_start: 0.7223 (mt) cc_final: 0.6954 (mt) REVERT: Q 260 PHE cc_start: 0.8030 (m-10) cc_final: 0.7526 (m-80) REVERT: Q 277 LYS cc_start: 0.9129 (mppt) cc_final: 0.8898 (mptt) REVERT: h 204 MET cc_start: 0.8226 (ppp) cc_final: 0.7217 (ppp) REVERT: h 282 MET cc_start: 0.7920 (ttm) cc_final: 0.7095 (mtp) REVERT: h 296 MET cc_start: 0.8357 (pmm) cc_final: 0.7500 (pmm) REVERT: h 297 LEU cc_start: 0.9116 (tp) cc_final: 0.8892 (tp) REVERT: i 30 HIS cc_start: 0.7156 (m90) cc_final: 0.6643 (p-80) REVERT: j 110 TYR cc_start: 0.9121 (m-10) cc_final: 0.8773 (t80) REVERT: k 204 MET cc_start: -0.3028 (tpt) cc_final: -0.3477 (mtt) REVERT: l 15 LYS cc_start: 0.9571 (mmtt) cc_final: 0.9162 (mmmt) REVERT: l 122 GLU cc_start: 0.9020 (pt0) cc_final: 0.8725 (pp20) REVERT: l 204 MET cc_start: 0.8744 (tpt) cc_final: 0.8076 (ppp) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2372 time to fit residues: 133.3544 Evaluate side-chains 260 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [375, 289, 215, 257, 185, 224, 276, 123, 461, 300, 40] chunk 375 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 185 optimal weight: 0.3980 chunk 224 optimal weight: 4.9990 chunk 276 optimal weight: 0.0980 chunk 123 optimal weight: 0.0870 chunk 461 optimal weight: 0.5980 chunk 300 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ah 334 GLN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 241 ASN ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 231 ASN ** j 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 278 ASN ** l 305 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 = 0.3863 r_free = 0.3863 target = 0.092848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066413 restraints weight = 308866.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065207 restraints weight = 177458.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065325 restraints weight = 115841.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.065413 restraints weight = 87767.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.065618 restraints weight = 68838.948| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.285 41134 Z= 0.384 Angle : 0.624 18.594 55935 Z= 0.323 Chirality : 0.040 0.199 6352 Planarity : 0.004 0.121 7175 Dihedral : 4.511 50.731 5597 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.51 % Favored : 93.33 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.56 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4976 helix: 1.72 (0.11), residues: 2279 sheet: -1.24 (0.23), residues: 524 loop : -2.32 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 131 TYR 0.044 0.001 TYR D 89 PHE 0.024 0.001 PHE M 260 TRP 0.022 0.001 TRP O 116 HIS 0.029 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00966 / 0.38 (41132) covalent geometry : angle 0.62297 / 0.32 (55931) SS BOND : bond 0.00873 / 0.42 ( 2) SS BOND : angle 5.00748 / 2.67 ( 4) hydrogen bonds : bond 0.03418 / 2.33 ( 1761) hydrogen bonds : angle 4.49966 / 3.17 ( 5088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 75 LYS cc_start: 0.9733 (tttt) cc_final: 0.9231 (pttt) REVERT: AJ 113 ASP cc_start: 0.8882 (t0) cc_final: 0.7932 (t0) REVERT: AJ 138 GLU cc_start: 0.9262 (pp20) cc_final: 0.8830 (pp20) REVERT: AJ 198 MET cc_start: 0.8887 (mmp) cc_final: 0.8587 (mmp) REVERT: AY 10 GLU cc_start: 0.7140 (tt0) cc_final: 0.6534 (tp30) REVERT: AY 44 ASN cc_start: 0.8223 (p0) cc_final: 0.8012 (p0) REVERT: AY 198 MET cc_start: 0.9379 (mmp) cc_final: 0.9175 (mmp) REVERT: Ah 64 MET cc_start: 0.8763 (ptt) cc_final: 0.8440 (ptt) REVERT: Ah 252 MET cc_start: 0.9347 (mmp) cc_final: 0.9037 (mmp) REVERT: Ah 335 MET cc_start: 0.8498 (pmm) cc_final: 0.8024 (ptp) REVERT: Ah 398 MET cc_start: 0.8333 (mtm) cc_final: 0.7511 (mtm) REVERT: Ah 405 MET cc_start: 0.8950 (ppp) cc_final: 0.8500 (ppp) REVERT: Ah 537 MET cc_start: 0.8520 (tpp) cc_final: 0.8166 (tpp) REVERT: Ao 202 ASP cc_start: 0.9374 (m-30) cc_final: 0.9010 (t0) REVERT: Ao 393 ASP cc_start: 0.8768 (t0) cc_final: 0.8428 (t0) REVERT: Ao 406 LYS cc_start: 0.9551 (ptpt) cc_final: 0.9210 (pttm) REVERT: Ao 407 GLN cc_start: 0.9331 (tt0) cc_final: 0.8600 (pt0) REVERT: Ao 408 MET cc_start: 0.9490 (mtp) cc_final: 0.9216 (mtp) REVERT: Ap 131 ARG cc_start: 0.8709 (ptp-110) cc_final: 0.8449 (ptt-90) REVERT: Ap 305 TYR cc_start: 0.9026 (m-80) cc_final: 0.8552 (m-80) REVERT: Ap 390 MET cc_start: 0.9645 (mtp) cc_final: 0.9307 (mtt) REVERT: Ap 394 MET cc_start: 0.9597 (ttp) cc_final: 0.8736 (mmp) REVERT: Ap 422 TYR cc_start: 0.9000 (m-80) cc_final: 0.8406 (m-10) REVERT: D 1 MET cc_start: 0.0918 (mtt) cc_final: 0.0096 (mtt) REVERT: D 139 ASP cc_start: 0.8588 (m-30) cc_final: 0.8214 (m-30) REVERT: D 167 MET cc_start: 0.8384 (mmm) cc_final: 0.7945 (mmm) REVERT: D 201 MET cc_start: 0.3718 (ttt) cc_final: 0.1210 (mmt) REVERT: D 462 LEU cc_start: 0.9385 (mt) cc_final: 0.9061 (tt) REVERT: D 481 ILE cc_start: 0.9307 (mt) cc_final: 0.8797 (mm) REVERT: M 36 PHE cc_start: 0.9330 (m-10) cc_final: 0.8794 (m-80) REVERT: M 186 MET cc_start: 0.8424 (ttt) cc_final: 0.8142 (tpt) REVERT: N 292 ARG cc_start: 0.8067 (mtt180) cc_final: 0.6453 (tpm170) REVERT: O 296 MET cc_start: 0.6873 (ttm) cc_final: 0.6355 (pmm) REVERT: P 186 MET cc_start: 0.6750 (tmm) cc_final: 0.5922 (mtt) REVERT: Q 260 PHE cc_start: 0.8137 (m-10) cc_final: 0.7736 (m-80) REVERT: Q 277 LYS cc_start: 0.9148 (mppt) cc_final: 0.8932 (mptt) REVERT: Q 296 MET cc_start: 0.8029 (pmm) cc_final: 0.7255 (pmm) REVERT: h 204 MET cc_start: 0.7999 (ppp) cc_final: 0.7021 (ppp) REVERT: h 282 MET cc_start: 0.7860 (ttm) cc_final: 0.7265 (mtp) REVERT: i 30 HIS cc_start: 0.7047 (m90) cc_final: 0.6528 (p-80) REVERT: i 186 MET cc_start: 0.7857 (mmm) cc_final: 0.7505 (mmm) REVERT: i 296 MET cc_start: 0.8037 (mmm) cc_final: 0.7831 (tpt) REVERT: j 110 TYR cc_start: 0.9092 (m-10) cc_final: 0.8810 (t80) REVERT: k 204 MET cc_start: -0.2836 (tpt) cc_final: -0.3291 (mtt) REVERT: l 186 MET cc_start: 0.8211 (ttt) cc_final: 0.7155 (tmm) REVERT: l 204 MET cc_start: 0.8647 (tpt) cc_final: 0.7908 (ppp) REVERT: l 256 THR cc_start: 0.8816 (m) cc_final: 0.8500 (m) outliers start: 1 outliers final: 1 residues processed: 365 average time/residue: 0.2362 time to fit residues: 142.1339 Evaluate side-chains 290 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [331, 210, 416, 485, 83, 137, 378, 325, 149, 235, 243] chunk 331 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 416 optimal weight: 8.9990 chunk 485 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 378 optimal weight: 0.9980 chunk 325 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AJ 89 GLN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 231 ASN i 102 HIS i 278 ASN j 176 GLN j 200 HIS ** l 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.090527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.064416 restraints weight = 315437.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.062290 restraints weight = 182988.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.062302 restraints weight = 121270.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.062477 restraints weight = 90562.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.062790 restraints weight = 72491.700| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.134 41134 Z= 0.419 Angle : 0.688 19.842 55935 Z= 0.362 Chirality : 0.041 0.285 6352 Planarity : 0.005 0.120 7175 Dihedral : 4.689 51.390 5597 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.24 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.12), residues: 4976 helix: 1.54 (0.11), residues: 2285 sheet: -1.67 (0.22), residues: 561 loop : -2.38 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 20 TYR 0.066 0.002 TYR D 89 PHE 0.026 0.002 PHE M 260 TRP 0.025 0.002 TRP O 116 HIS 0.046 0.002 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01012 / 0.42 (41132) covalent geometry : angle 0.68608 / 0.36 (55931) SS BOND : bond 0.01050 / 0.51 ( 2) SS BOND : angle 5.98224 / 3.28 ( 4) hydrogen bonds : bond 0.03737 / 2.56 ( 1761) hydrogen bonds : angle 4.78792 / 3.37 ( 5088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AJ 59 ARG cc_start: 0.9225 (mtp85) cc_final: 0.8977 (mtp85) REVERT: AJ 75 LYS cc_start: 0.9735 (tttt) cc_final: 0.9257 (pttt) REVERT: AJ 113 ASP cc_start: 0.8711 (t0) cc_final: 0.7807 (t0) REVERT: AJ 138 GLU cc_start: 0.9162 (pp20) cc_final: 0.8856 (pp20) REVERT: AJ 198 MET cc_start: 0.8991 (mmp) cc_final: 0.8729 (mmm) REVERT: AJ 204 ASP cc_start: 0.8449 (m-30) cc_final: 0.8161 (m-30) REVERT: AY 10 GLU cc_start: 0.7254 (tt0) cc_final: 0.6633 (tp30) REVERT: AY 44 ASN cc_start: 0.8366 (p0) cc_final: 0.8151 (p0) REVERT: Ah 64 MET cc_start: 0.8749 (ptt) cc_final: 0.8251 (ptt) REVERT: Ah 252 MET cc_start: 0.9394 (mmp) cc_final: 0.9108 (mmm) REVERT: Ah 335 MET cc_start: 0.8491 (pmm) cc_final: 0.7934 (ptp) REVERT: Ah 398 MET cc_start: 0.8436 (mtm) cc_final: 0.7681 (mtm) REVERT: Ah 405 MET cc_start: 0.8920 (ppp) cc_final: 0.8441 (ppp) REVERT: Ah 437 MET cc_start: 0.8773 (pmm) cc_final: 0.8561 (pmm) REVERT: Ah 461 MET cc_start: 0.8573 (tmm) cc_final: 0.8349 (tmm) REVERT: Ah 537 MET cc_start: 0.8613 (tpp) cc_final: 0.8253 (tpp) REVERT: Ah 621 LYS cc_start: 0.9337 (ptpt) cc_final: 0.8975 (ptpp) REVERT: Ah 623 MET cc_start: 0.7996 (tpt) cc_final: 0.7635 (tpt) REVERT: Ao 202 ASP cc_start: 0.9349 (m-30) cc_final: 0.9094 (t0) REVERT: Ao 206 ARG cc_start: 0.9267 (mtt180) cc_final: 0.8967 (mmm160) REVERT: Ao 244 PHE cc_start: 0.9406 (t80) cc_final: 0.9127 (t80) REVERT: Ao 384 MET cc_start: 0.7569 (tpp) cc_final: 0.7133 (tpp) REVERT: Ao 393 ASP cc_start: 0.8908 (t0) cc_final: 0.8647 (t0) REVERT: Ao 406 LYS cc_start: 0.9568 (ptpt) cc_final: 0.9148 (pttm) REVERT: Ao 408 MET cc_start: 0.9504 (mtp) cc_final: 0.9245 (mtt) REVERT: Ap 208 LEU cc_start: 0.9620 (pp) cc_final: 0.9416 (pp) REVERT: Ap 212 HIS cc_start: 0.8404 (m-70) cc_final: 0.8060 (m90) REVERT: Ap 390 MET cc_start: 0.9649 (mtp) cc_final: 0.9346 (mtt) REVERT: Ap 394 MET cc_start: 0.9614 (ttp) cc_final: 0.8712 (mmp) REVERT: Ap 422 TYR cc_start: 0.9068 (m-80) cc_final: 0.8650 (m-10) REVERT: D 1 MET cc_start: 0.1479 (mtt) cc_final: 0.0412 (mtt) REVERT: D 167 MET cc_start: 0.8479 (mmm) cc_final: 0.8053 (mmm) REVERT: D 201 MET cc_start: 0.4103 (ttt) cc_final: 0.1349 (mmt) REVERT: D 212 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7482 (ptpt) REVERT: D 462 LEU cc_start: 0.9388 (mt) cc_final: 0.9010 (tt) REVERT: M 36 PHE cc_start: 0.9378 (m-10) cc_final: 0.8864 (m-80) REVERT: M 110 TYR cc_start: 0.9186 (m-80) cc_final: 0.8979 (m-80) REVERT: M 126 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8970 (tm-30) REVERT: N 292 ARG cc_start: 0.8349 (mtt180) cc_final: 0.6535 (tpm170) REVERT: O 296 MET cc_start: 0.6394 (ttm) cc_final: 0.5827 (pmm) REVERT: P 186 MET cc_start: 0.6842 (tmm) cc_final: 0.6028 (mtt) REVERT: Q 260 PHE cc_start: 0.8031 (m-10) cc_final: 0.7468 (m-80) REVERT: Q 277 LYS cc_start: 0.9131 (mppt) cc_final: 0.8812 (mptt) REVERT: Q 296 MET cc_start: 0.8095 (pmm) cc_final: 0.7387 (pmm) REVERT: h 204 MET cc_start: 0.8130 (ppp) cc_final: 0.7149 (ppp) REVERT: h 282 MET cc_start: 0.7908 (ttm) cc_final: 0.7061 (mtp) REVERT: i 30 HIS cc_start: 0.6760 (m90) cc_final: 0.6100 (p-80) REVERT: i 296 MET cc_start: 0.7917 (mmm) cc_final: 0.7639 (tpt) REVERT: j 110 TYR cc_start: 0.9098 (m-10) cc_final: 0.8782 (t80) REVERT: k 204 MET cc_start: -0.2808 (tpt) cc_final: -0.3256 (mtt) REVERT: l 186 MET cc_start: 0.8200 (ttt) cc_final: 0.7151 (tmm) REVERT: l 204 MET cc_start: 0.8594 (tpt) cc_final: 0.8016 (ppp) REVERT: l 256 THR cc_start: 0.8815 (m) cc_final: 0.8287 (m) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2353 time to fit residues: 128.5193 Evaluate side-chains 266 residues out of total 4392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: [204, 374, 477, 490, 186, 49, 247, 142, 167, 51, 290] chunk 204 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 490 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 247 optimal weight: 0.0070 chunk 142 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AJ 89 GLN AJ 139 GLN AY 223 GLN Ah 265 GLN Ah 334 GLN ** Ap 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 102 HIS ** l 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.091710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065333 restraints weight = 312838.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.063011 restraints weight = 177149.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063205 restraints weight = 117743.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.063405 restraints weight = 85720.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063773 restraints weight = 71974.071| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.123 41134 Z= 0.388 Angle : 0.628 19.820 55935 Z= 0.330 Chirality : 0.040 0.281 6352 Planarity : 0.004 0.121 7175 Dihedral : 4.533 50.531 5597 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.19 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.02 % Twisted Proline : 0.84 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4976 helix: 1.63 (0.11), residues: 2290 sheet: -1.44 (0.22), residues: 533 loop : -2.32 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAp 82 TYR 0.066 0.001 TYR D 89 PHE 0.034 0.001 PHE i 23 TRP 0.023 0.001 TRP O 116 HIS 0.045 0.001 HISAJ 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00959 / 0.39 (41132) covalent geometry : angle 0.62615 / 0.33 (55931) SS BOND : bond 0.01219 / 0.59 ( 2) SS BOND : angle 5.84886 / 3.17 ( 4) hydrogen bonds : bond 0.03490 / 2.41 ( 1761) hydrogen bonds : angle 4.58297 / 3.23 ( 5088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12527.67 seconds wall clock time: 214 minutes 12.46 seconds (12852.46 seconds total)