Starting phenix.real_space_refine on Tue Nov 19 12:32:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6njp_9391/11_2024/6njp_9391.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 12408 2.51 5 N 3389 2.21 5 O 3702 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3169 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3106 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 12.01, per 1000 atoms: 0.61 Number of scatterers: 19607 At special positions: 0 Unit cell: (123.42, 118.32, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 80 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3702 8.00 N 3389 7.00 C 12408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 41.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 236 through 257 removed outlier: 4.754A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.511A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.997A pdb=" N PHE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 373 through 398 removed outlier: 3.544A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.519A pdb=" N LYS A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.890A pdb=" N ALA A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 4.037A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 111' Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.197A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 238 through 257 removed outlier: 5.398A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 282 removed outlier: 3.969A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 removed outlier: 4.067A pdb=" N PHE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.049A pdb=" N VAL B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.762A pdb=" N VAL B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 424 removed outlier: 5.332A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.516A pdb=" N ALA B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.829A pdb=" N LEU C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 111 " --> pdb=" O ASP C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.894A pdb=" N ARG C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.973A pdb=" N ASN C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 218 removed outlier: 3.817A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 218 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 267 through 282 removed outlier: 4.126A pdb=" N TYR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.982A pdb=" N PHE C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 373 through 400 removed outlier: 4.969A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 removed outlier: 3.678A pdb=" N ASP C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.823A pdb=" N ALA C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 236 through 257 removed outlier: 5.436A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.150A pdb=" N TYR D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.930A pdb=" N PHE D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 373 through 394 Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.745A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.934A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.507A pdb=" N ALA D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 236 through 257 removed outlier: 5.264A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 281 removed outlier: 4.020A pdb=" N TYR E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 303 removed outlier: 4.135A pdb=" N PHE E 296 " --> pdb=" O PRO E 292 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 346 through 351 removed outlier: 3.649A pdb=" N ALA E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 394 removed outlier: 4.123A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 407 through 416 removed outlier: 3.559A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 424 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.907A pdb=" N LEU F 110 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F 111 " --> pdb=" O ASP F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 111' Processing helix chain 'F' and resid 143 through 147 removed outlier: 3.692A pdb=" N LEU F 146 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG F 147 " --> pdb=" O PRO F 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 147' Processing helix chain 'F' and resid 158 through 165 removed outlier: 3.760A pdb=" N ASP F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.834A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 236 through 256 removed outlier: 4.890A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 Processing helix chain 'F' and resid 292 through 305 removed outlier: 3.963A pdb=" N PHE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) Proline residue: F 300 - end of helix removed outlier: 4.179A pdb=" N ARG F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 337 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.621A pdb=" N LEU F 362 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 363 " --> pdb=" O ILE F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 363' Processing helix chain 'F' and resid 373 through 389 Processing helix chain 'F' and resid 390 through 399 removed outlier: 4.132A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.845A pdb=" N ALA F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS F 415 " --> pdb=" O ASP F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 424 Processing helix chain 'F' and resid 433 through 443 removed outlier: 3.668A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 26 removed outlier: 3.534A pdb=" N ILE G 5 " --> pdb=" O MET G 1 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 114 removed outlier: 3.741A pdb=" N ASP G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.875A pdb=" N LYS A 37 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 79 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 71 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 66 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.628A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 198 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET A 264 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 200 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP A 266 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 202 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 317 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 263 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR A 319 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N MET A 265 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LEU A 321 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.636A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 81 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 70 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 66 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 115 removed outlier: 5.711A pdb=" N ILE B 115 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR B 232 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 205 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 115 removed outlier: 5.711A pdb=" N ILE B 115 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR B 232 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 205 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 154 removed outlier: 4.464A pdb=" N CYS B 167 " --> pdb=" O PHE B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41 removed outlier: 3.792A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 79 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 66 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 36 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.919A pdb=" N ARG C 113 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 228 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 199 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 229 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 201 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 198 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET C 264 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 200 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 317 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 263 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR C 319 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET C 265 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU C 321 " --> pdb=" O MET C 265 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 173 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 320 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 175 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 174 " --> pdb=" O ILE C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.402A pdb=" N CYS C 167 " --> pdb=" O PHE C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 5.730A pdb=" N ILE D 38 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG D 49 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 72 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE D 58 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.534A pdb=" N ILE D 198 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET D 264 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 200 " --> pdb=" O MET D 264 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP D 266 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA D 202 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 173 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL D 320 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 175 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY D 341 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.221A pdb=" N CYS D 167 " --> pdb=" O PHE D 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 60 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 97 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 73 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU F 77 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE F 73 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE F 79 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 103 through 106 Processing sheet with id=AC2, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE E 173 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E 320 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE E 175 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 343 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY E 174 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.570A pdb=" N CYS E 167 " --> pdb=" O PHE E 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 115 removed outlier: 5.850A pdb=" N ILE F 115 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR F 232 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 201 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE F 204 " --> pdb=" O ASP F 266 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 261 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE F 317 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 263 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR F 319 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET F 265 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU F 321 " --> pdb=" O MET F 265 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2328 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: 6.27 Time building geometry restraints manager: 5.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4177 1.33 - 1.45: 3979 1.45 - 1.57: 11595 1.57 - 1.69: 20 1.69 - 1.81: 134 Bond restraints: 19905 Sorted by residual: bond pdb=" F1 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.734 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" F1 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" F1 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA A 139 " pdb=" N GLU A 140 " ideal model delta sigma weight residual 1.329 1.272 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 19900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 26069 2.84 - 5.68: 758 5.68 - 8.52: 75 8.52 - 11.36: 29 11.36 - 14.19: 7 Bond angle restraints: 26938 Sorted by residual: angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C SER B 313 " pdb=" N ILE B 314 " pdb=" CA ILE B 314 " ideal model delta sigma weight residual 123.19 117.56 5.63 1.24e+00 6.50e-01 2.06e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 113.16 106.42 6.74 1.49e+00 4.50e-01 2.05e+01 angle pdb=" C TYR F 97 " pdb=" N GLN F 98 " pdb=" CA GLN F 98 " ideal model delta sigma weight residual 122.61 129.48 -6.87 1.56e+00 4.11e-01 1.94e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 26933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 11964 30.15 - 60.30: 192 60.30 - 90.45: 16 90.45 - 120.60: 0 120.60 - 150.75: 4 Dihedral angle restraints: 12176 sinusoidal: 4949 harmonic: 7227 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 90.75 -150.75 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 89.03 -149.03 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 600 " pdb=" O5' ADP C 600 " pdb=" PA ADP C 600 " pdb=" O2A ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 87.67 -147.67 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 12173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2736 0.097 - 0.193: 349 0.193 - 0.290: 29 0.290 - 0.386: 3 0.386 - 0.483: 2 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CB ILE F 204 " pdb=" CA ILE F 204 " pdb=" CG1 ILE F 204 " pdb=" CG2 ILE F 204 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 3116 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 132 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 330 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 83 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C PHE F 83 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE F 83 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU F 84 " -0.015 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 5 2.00 - 2.73: 1287 2.73 - 3.45: 26664 3.45 - 4.18: 45810 4.18 - 4.90: 84379 Nonbonded interactions: 158145 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.276 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.814 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.842 2.170 nonbonded pdb=" OG SER D 184 " pdb="MG MG D 601 " model vdw 1.954 2.170 nonbonded pdb=" OG SER E 184 " pdb="MG MG E 601 " model vdw 1.983 2.170 ... (remaining 158140 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 'A' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'D' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'E' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.060 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.097 19905 Z= 0.570 Angle : 1.171 14.194 26938 Z= 0.622 Chirality : 0.066 0.483 3119 Planarity : 0.008 0.069 3473 Dihedral : 11.572 150.745 7536 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.67 % Allowed : 5.67 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.13), residues: 2512 helix: -3.08 (0.12), residues: 937 sheet: -1.90 (0.23), residues: 431 loop : -2.53 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.010 0.002 HIS D 342 PHE 0.039 0.004 PHE D 83 TYR 0.021 0.003 TYR A 90 ARG 0.013 0.001 ARG E 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 353 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.6704 (m-80) cc_final: 0.6289 (m-80) REVERT: A 97 TYR cc_start: 0.7059 (t80) cc_final: 0.6726 (t80) REVERT: A 241 MET cc_start: 0.8515 (ttp) cc_final: 0.8238 (ttt) REVERT: A 311 LYS cc_start: 0.8945 (tttp) cc_final: 0.8554 (ttpt) REVERT: A 378 ARG cc_start: 0.7334 (ppp-140) cc_final: 0.7122 (ttm-80) REVERT: A 392 ASN cc_start: 0.7652 (t0) cc_final: 0.7429 (t0) REVERT: B 66 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7815 (mtm180) REVERT: B 80 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 401 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 407 ASP cc_start: 0.6656 (t70) cc_final: 0.6229 (t70) REVERT: C 35 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: C 54 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7682 (mmm-85) REVERT: C 74 ASP cc_start: 0.7667 (t70) cc_final: 0.7458 (t0) REVERT: C 116 ASP cc_start: 0.7687 (t0) cc_final: 0.7469 (t0) REVERT: C 151 ASP cc_start: 0.8015 (p0) cc_final: 0.7784 (p0) REVERT: C 260 ASN cc_start: 0.8156 (m-40) cc_final: 0.7288 (t0) REVERT: C 378 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7623 (mtm110) REVERT: D 66 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6525 (mtm180) REVERT: D 85 HIS cc_start: 0.8222 (p90) cc_final: 0.7428 (m-70) REVERT: D 348 GLU cc_start: 0.8122 (pp20) cc_final: 0.7812 (pm20) REVERT: E 47 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8122 (ttmt) REVERT: E 415 LYS cc_start: 0.8672 (ttpm) cc_final: 0.8419 (ttmm) REVERT: F 54 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6790 (mtt180) REVERT: F 77 GLU cc_start: 0.6243 (mp0) cc_final: 0.5924 (mp0) REVERT: F 368 MET cc_start: 0.6861 (mtm) cc_final: 0.6624 (mtp) REVERT: F 422 ASN cc_start: 0.7717 (p0) cc_final: 0.7444 (p0) outliers start: 14 outliers final: 4 residues processed: 365 average time/residue: 0.3783 time to fit residues: 198.9464 Evaluate side-chains 234 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.5980 chunk 190 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 128 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN C 98 GLN D 416 ASN D 421 GLN E 376 HIS F 98 GLN G 26 GLN G 106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19905 Z= 0.165 Angle : 0.647 12.089 26938 Z= 0.318 Chirality : 0.045 0.169 3119 Planarity : 0.005 0.055 3473 Dihedral : 7.549 136.650 2811 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.57 % Allowed : 9.15 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.15), residues: 2512 helix: -1.28 (0.15), residues: 971 sheet: -1.54 (0.24), residues: 423 loop : -2.20 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 94 HIS 0.005 0.001 HIS F 354 PHE 0.027 0.001 PHE D 58 TYR 0.018 0.001 TYR A 390 ARG 0.005 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8060 (mp) cc_final: 0.7664 (mm) REVERT: A 215 LEU cc_start: 0.7511 (pp) cc_final: 0.7263 (mt) REVERT: A 241 MET cc_start: 0.8262 (ttp) cc_final: 0.7947 (ttt) REVERT: A 311 LYS cc_start: 0.8882 (tttp) cc_final: 0.8448 (ttpt) REVERT: A 378 ARG cc_start: 0.7374 (ppp-140) cc_final: 0.7135 (ttm-80) REVERT: A 392 ASN cc_start: 0.7676 (t0) cc_final: 0.7412 (t0) REVERT: A 416 ASN cc_start: 0.7840 (m-40) cc_final: 0.7583 (m110) REVERT: B 80 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 162 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 348 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: B 394 GLU cc_start: 0.7392 (pt0) cc_final: 0.6872 (tt0) REVERT: B 407 ASP cc_start: 0.6592 (t70) cc_final: 0.6161 (t70) REVERT: C 35 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: C 54 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7436 (mmm-85) REVERT: C 116 ASP cc_start: 0.7620 (t0) cc_final: 0.7365 (t0) REVERT: C 151 ASP cc_start: 0.7894 (p0) cc_final: 0.7675 (p0) REVERT: C 260 ASN cc_start: 0.7964 (m-40) cc_final: 0.7137 (t0) REVERT: C 382 GLU cc_start: 0.7561 (tt0) cc_final: 0.7214 (tt0) REVERT: D 126 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5915 (pp) REVERT: D 346 THR cc_start: 0.8752 (m) cc_final: 0.8420 (p) REVERT: D 348 GLU cc_start: 0.7996 (pp20) cc_final: 0.7701 (pm20) REVERT: E 74 ASP cc_start: 0.6728 (t70) cc_final: 0.6451 (t70) REVERT: E 122 MET cc_start: 0.7241 (ttp) cc_final: 0.7030 (mtp) REVERT: E 238 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7865 (pt) REVERT: E 329 ASP cc_start: 0.7482 (t70) cc_final: 0.6930 (m-30) REVERT: E 411 ASP cc_start: 0.7750 (t0) cc_final: 0.7068 (m-30) REVERT: E 433 SER cc_start: 0.8378 (t) cc_final: 0.8059 (p) REVERT: F 54 ARG cc_start: 0.7118 (mtp-110) cc_final: 0.6904 (ttt180) REVERT: F 386 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5856 (mp) outliers start: 54 outliers final: 19 residues processed: 325 average time/residue: 0.3556 time to fit residues: 169.5748 Evaluate side-chains 260 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 203 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 257 GLN F 426 GLN G 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19905 Z= 0.294 Angle : 0.693 9.911 26938 Z= 0.338 Chirality : 0.048 0.171 3119 Planarity : 0.005 0.048 3473 Dihedral : 7.375 132.798 2810 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.38 % Allowed : 11.53 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.16), residues: 2512 helix: -0.64 (0.16), residues: 987 sheet: -1.35 (0.25), residues: 427 loop : -2.00 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 94 HIS 0.006 0.001 HIS D 342 PHE 0.023 0.002 PHE D 58 TYR 0.019 0.002 TYR F 390 ARG 0.005 0.001 ARG C 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 240 time to evaluate : 2.460 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 90 TYR cc_start: 0.6428 (m-80) cc_final: 0.5957 (m-80) REVERT: A 97 TYR cc_start: 0.7369 (t80) cc_final: 0.7083 (t80) REVERT: A 102 PHE cc_start: 0.8167 (t80) cc_final: 0.7568 (t80) REVERT: A 215 LEU cc_start: 0.7678 (pp) cc_final: 0.7349 (mt) REVERT: A 217 LEU cc_start: 0.8678 (tt) cc_final: 0.8320 (tp) REVERT: A 241 MET cc_start: 0.8468 (ttp) cc_final: 0.8182 (ttt) REVERT: A 317 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8319 (mt) REVERT: A 378 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7186 (ttm-80) REVERT: A 392 ASN cc_start: 0.7665 (t0) cc_final: 0.7449 (t0) REVERT: A 416 ASN cc_start: 0.7908 (m-40) cc_final: 0.7690 (m110) REVERT: B 37 LYS cc_start: 0.8238 (mttm) cc_final: 0.7972 (mmtp) REVERT: B 162 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (t0) REVERT: B 348 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: B 394 GLU cc_start: 0.7424 (pt0) cc_final: 0.7171 (pt0) REVERT: B 407 ASP cc_start: 0.6817 (t70) cc_final: 0.6351 (t70) REVERT: C 54 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7624 (mmm-85) REVERT: C 105 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8431 (ttm-80) REVERT: C 116 ASP cc_start: 0.7624 (t0) cc_final: 0.7354 (t0) REVERT: C 378 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7375 (ttp80) REVERT: C 382 GLU cc_start: 0.7490 (tt0) cc_final: 0.7255 (tt0) REVERT: C 431 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7313 (mm) REVERT: D 113 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7725 (mtt-85) REVERT: D 346 THR cc_start: 0.8740 (m) cc_final: 0.8488 (p) REVERT: D 348 GLU cc_start: 0.7984 (pp20) cc_final: 0.7762 (pm20) REVERT: D 368 MET cc_start: 0.8881 (ttp) cc_final: 0.8675 (ttt) REVERT: E 411 ASP cc_start: 0.7642 (t0) cc_final: 0.7296 (m-30) REVERT: F 54 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6773 (ttt180) REVERT: F 132 PRO cc_start: 0.8633 (Cg_endo) cc_final: 0.8210 (Cg_exo) REVERT: F 234 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: F 375 GLU cc_start: 0.7802 (pt0) cc_final: 0.7582 (pt0) REVERT: F 377 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.6002 (pp) REVERT: F 418 LYS cc_start: 0.7106 (tppt) cc_final: 0.6779 (tppt) REVERT: F 426 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7543 (pt0) outliers start: 71 outliers final: 36 residues processed: 300 average time/residue: 0.3547 time to fit residues: 158.3448 Evaluate side-chains 270 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 426 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN G 24 ASN G 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19905 Z= 0.274 Angle : 0.669 9.219 26938 Z= 0.324 Chirality : 0.047 0.198 3119 Planarity : 0.005 0.046 3473 Dihedral : 7.101 133.001 2807 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.91 % Allowed : 12.96 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.16), residues: 2512 helix: -0.26 (0.17), residues: 970 sheet: -1.26 (0.25), residues: 419 loop : -1.82 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 94 HIS 0.007 0.001 HIS F 354 PHE 0.024 0.002 PHE D 58 TYR 0.016 0.002 TYR A 390 ARG 0.005 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 234 time to evaluate : 2.042 Fit side-chains REVERT: A 102 PHE cc_start: 0.8164 (t80) cc_final: 0.7725 (t80) REVERT: A 215 LEU cc_start: 0.7633 (pp) cc_final: 0.7323 (mt) REVERT: A 217 LEU cc_start: 0.8727 (tt) cc_final: 0.8302 (tp) REVERT: A 241 MET cc_start: 0.8455 (ttp) cc_final: 0.8162 (ttt) REVERT: A 317 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 416 ASN cc_start: 0.7914 (m-40) cc_final: 0.7686 (m110) REVERT: B 37 LYS cc_start: 0.8311 (mttm) cc_final: 0.8050 (mmtp) REVERT: B 286 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7860 (t0) REVERT: B 394 GLU cc_start: 0.7394 (pt0) cc_final: 0.7189 (pt0) REVERT: B 407 ASP cc_start: 0.6684 (t70) cc_final: 0.6243 (t70) REVERT: C 35 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: C 54 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7680 (mmm-85) REVERT: C 116 ASP cc_start: 0.7573 (t0) cc_final: 0.7267 (t0) REVERT: C 382 GLU cc_start: 0.7354 (tt0) cc_final: 0.7141 (tt0) REVERT: C 431 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7462 (mm) REVERT: D 113 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7683 (mtt-85) REVERT: D 122 MET cc_start: 0.8205 (mmm) cc_final: 0.7958 (mtp) REVERT: E 74 ASP cc_start: 0.6761 (t70) cc_final: 0.6496 (t70) REVERT: E 401 GLU cc_start: 0.7366 (pt0) cc_final: 0.7157 (pt0) REVERT: E 404 MET cc_start: 0.7608 (tpp) cc_final: 0.7028 (tpp) REVERT: E 411 ASP cc_start: 0.7604 (t0) cc_final: 0.7358 (t0) REVERT: F 54 ARG cc_start: 0.7049 (mtp180) cc_final: 0.6783 (ttt180) REVERT: F 234 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: F 375 GLU cc_start: 0.7829 (pt0) cc_final: 0.7605 (pt0) REVERT: F 382 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: F 418 LYS cc_start: 0.6986 (tppt) cc_final: 0.6606 (tppt) outliers start: 82 outliers final: 48 residues processed: 302 average time/residue: 0.3693 time to fit residues: 165.3129 Evaluate side-chains 267 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 444 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 19905 Z= 0.432 Angle : 0.756 9.783 26938 Z= 0.368 Chirality : 0.051 0.191 3119 Planarity : 0.005 0.049 3473 Dihedral : 7.348 134.436 2805 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.24 % Allowed : 14.35 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.16), residues: 2512 helix: -0.41 (0.17), residues: 972 sheet: -1.28 (0.25), residues: 439 loop : -1.79 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 94 HIS 0.008 0.002 HIS D 342 PHE 0.022 0.002 PHE D 58 TYR 0.017 0.002 TYR C 402 ARG 0.006 0.001 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 223 time to evaluate : 2.705 Fit side-chains revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7808 (tp) REVERT: A 215 LEU cc_start: 0.7806 (pp) cc_final: 0.7389 (mt) REVERT: A 241 MET cc_start: 0.8513 (ttp) cc_final: 0.8235 (ttt) REVERT: A 317 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8359 (mt) REVERT: B 41 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 280 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 286 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8003 (t0) REVERT: C 35 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6412 (mp0) REVERT: C 54 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7714 (mmm-85) REVERT: C 116 ASP cc_start: 0.7655 (t0) cc_final: 0.7296 (t0) REVERT: C 431 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7585 (mm) REVERT: D 378 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7132 (tpp-160) REVERT: E 74 ASP cc_start: 0.6842 (t70) cc_final: 0.6611 (t70) REVERT: F 54 ARG cc_start: 0.7228 (mtp180) cc_final: 0.6934 (ttt180) REVERT: F 234 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: F 375 GLU cc_start: 0.7946 (pt0) cc_final: 0.7707 (pt0) REVERT: F 390 TYR cc_start: 0.6280 (t80) cc_final: 0.6041 (t80) REVERT: F 418 LYS cc_start: 0.7096 (tppt) cc_final: 0.6710 (tppt) REVERT: F 426 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7474 (pt0) outliers start: 89 outliers final: 52 residues processed: 299 average time/residue: 0.4036 time to fit residues: 179.2447 Evaluate side-chains 265 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 426 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 242 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19905 Z= 0.192 Angle : 0.621 11.568 26938 Z= 0.299 Chirality : 0.046 0.182 3119 Planarity : 0.004 0.048 3473 Dihedral : 6.756 130.561 2805 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.38 % Allowed : 15.87 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2512 helix: 0.08 (0.17), residues: 967 sheet: -1.22 (0.25), residues: 424 loop : -1.62 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 94 HIS 0.006 0.001 HIS F 354 PHE 0.023 0.001 PHE D 58 TYR 0.017 0.001 TYR C 390 ARG 0.005 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 2.438 Fit side-chains REVERT: A 215 LEU cc_start: 0.7494 (pp) cc_final: 0.7272 (mt) REVERT: A 241 MET cc_start: 0.8427 (ttp) cc_final: 0.8088 (ttt) REVERT: A 317 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8320 (mt) REVERT: B 286 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7798 (t0) REVERT: B 414 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7284 (mp) REVERT: C 35 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: C 54 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7609 (mmm-85) REVERT: C 116 ASP cc_start: 0.7547 (t0) cc_final: 0.7268 (t0) REVERT: C 382 GLU cc_start: 0.7386 (tt0) cc_final: 0.6896 (tt0) REVERT: C 431 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 378 ARG cc_start: 0.7552 (ttm110) cc_final: 0.7063 (tpp-160) REVERT: E 74 ASP cc_start: 0.6893 (t70) cc_final: 0.6610 (t70) REVERT: F 54 ARG cc_start: 0.7127 (mtp180) cc_final: 0.6803 (ttt180) REVERT: F 69 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6082 (mt-10) REVERT: F 234 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: F 375 GLU cc_start: 0.7840 (pt0) cc_final: 0.7599 (pt0) outliers start: 71 outliers final: 43 residues processed: 283 average time/residue: 0.3582 time to fit residues: 149.2917 Evaluate side-chains 257 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 241 optimal weight: 30.0000 chunk 151 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19905 Z= 0.224 Angle : 0.638 10.137 26938 Z= 0.307 Chirality : 0.046 0.176 3119 Planarity : 0.004 0.048 3473 Dihedral : 6.533 124.913 2805 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.67 % Allowed : 16.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2512 helix: 0.25 (0.17), residues: 968 sheet: -1.16 (0.25), residues: 424 loop : -1.57 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 94 HIS 0.006 0.001 HIS F 354 PHE 0.030 0.001 PHE G 117 TYR 0.021 0.002 TYR F 390 ARG 0.004 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 223 time to evaluate : 2.519 Fit side-chains REVERT: A 215 LEU cc_start: 0.7521 (pp) cc_final: 0.7280 (mt) REVERT: A 317 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8325 (mt) REVERT: A 401 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: B 41 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 286 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 414 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7246 (mp) REVERT: C 35 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: C 54 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7640 (mmm-85) REVERT: C 116 ASP cc_start: 0.7594 (t0) cc_final: 0.7299 (t0) REVERT: C 382 GLU cc_start: 0.7444 (tt0) cc_final: 0.6893 (tt0) REVERT: C 431 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7640 (mm) REVERT: C 435 GLU cc_start: 0.7448 (pm20) cc_final: 0.6858 (pm20) REVERT: D 378 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7075 (tpp-160) REVERT: E 65 GLN cc_start: 0.6729 (tp40) cc_final: 0.6486 (tp-100) REVERT: E 74 ASP cc_start: 0.6881 (t70) cc_final: 0.6604 (t70) REVERT: F 54 ARG cc_start: 0.7062 (mtp180) cc_final: 0.6703 (ttt180) REVERT: F 69 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6127 (mt-10) REVERT: F 234 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7484 (m-30) outliers start: 77 outliers final: 53 residues processed: 289 average time/residue: 0.3690 time to fit residues: 158.0781 Evaluate side-chains 269 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 207 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19905 Z= 0.305 Angle : 0.677 9.565 26938 Z= 0.328 Chirality : 0.048 0.186 3119 Planarity : 0.005 0.053 3473 Dihedral : 6.633 125.042 2805 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.67 % Allowed : 16.49 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2512 helix: 0.14 (0.17), residues: 973 sheet: -1.21 (0.25), residues: 425 loop : -1.53 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 94 HIS 0.007 0.001 HIS F 354 PHE 0.030 0.002 PHE G 117 TYR 0.020 0.002 TYR C 402 ARG 0.008 0.000 ARG C 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 2.342 Fit side-chains REVERT: A 102 PHE cc_start: 0.7918 (t80) cc_final: 0.7643 (t80) REVERT: A 215 LEU cc_start: 0.7587 (pp) cc_final: 0.7293 (mt) REVERT: A 317 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8340 (mt) REVERT: A 401 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: A 416 ASN cc_start: 0.7957 (m-40) cc_final: 0.7752 (m110) REVERT: B 41 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 280 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8777 (mp) REVERT: B 286 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7877 (t0) REVERT: B 414 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7401 (mp) REVERT: C 35 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: C 54 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7675 (mmm-85) REVERT: C 116 ASP cc_start: 0.7611 (t0) cc_final: 0.7275 (t0) REVERT: C 431 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7646 (mm) REVERT: D 96 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (p) REVERT: D 378 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7089 (tpp-160) REVERT: E 152 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7799 (mm-40) REVERT: F 54 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6681 (ttt180) REVERT: F 234 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: F 299 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8726 (tp) REVERT: F 377 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6228 (pp) REVERT: F 418 LYS cc_start: 0.7229 (tppt) cc_final: 0.7017 (tppt) outliers start: 77 outliers final: 54 residues processed: 281 average time/residue: 0.3585 time to fit residues: 150.8928 Evaluate side-chains 269 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 213 optimal weight: 0.1980 chunk 224 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2982 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: