Starting phenix.real_space_refine on Sun Mar 24 00:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fkh_4271/03_2024/6fkh_4271_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 129 5.16 5 C 24906 2.51 5 N 6683 2.21 5 O 7495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 59": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 297": "NH1" <-> "NH2" Residue "E GLU 419": "OE1" <-> "OE2" Residue "E ARG 455": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "S GLU 37": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "K GLU 37": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "p GLU 169": "OE1" <-> "OE2" Residue "b ARG 59": "NH1" <-> "NH2" Residue "b ARG 71": "NH1" <-> "NH2" Residue "b ARG 82": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39231 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "C" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3858 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "p" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1299 Classifications: {'peptide': 161} Link IDs: {'TRANS': 160} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.94, per 1000 atoms: 0.48 Number of scatterers: 39231 At special positions: 0 Unit cell: (131.625, 141.102, 233.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 129 16.00 P 13 15.00 Mg 5 11.99 O 7495 8.00 N 6683 7.00 C 24906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.70 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.66 Conformation dependent library (CDL) restraints added in 7.5 seconds 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9452 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 28 sheets defined 56.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.95 Creating SS restraints... Processing helix chain 'a' and resid 37 through 57 Processing helix chain 'a' and resid 69 through 87 Processing helix chain 'a' and resid 95 through 114 removed outlier: 3.573A pdb=" N ILE a 105 " --> pdb=" O MET a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 155 Processing helix chain 'a' and resid 169 through 207 Proline residue: a 173 - end of helix removed outlier: 3.697A pdb=" N LYS a 182 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 3.654A pdb=" N LEU a 186 " --> pdb=" O PRO a 183 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG a 189 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU a 190 " --> pdb=" O SER a 187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY a 192 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE a 194 " --> pdb=" O PHE a 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL a 203 " --> pdb=" O VAL a 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU a 204 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER a 206 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 243 Proline residue: a 215 - end of helix removed outlier: 4.008A pdb=" N GLY a 225 " --> pdb=" O PHE a 222 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN a 227 " --> pdb=" O SER a 224 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE a 230 " --> pdb=" O GLN a 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 18 Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.721A pdb=" N MET C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 removed outlier: 3.745A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 233 through 253 Proline residue: C 240 - end of helix removed outlier: 3.609A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 removed outlier: 3.707A pdb=" N ALA C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 350 No H-bonds generated for 'chain 'C' and resid 347 through 350' Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 374 through 392 removed outlier: 3.598A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 removed outlier: 4.097A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 400 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER C 401 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.675A pdb=" N ARG C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.664A pdb=" N ASN C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 4.087A pdb=" N ARG C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 456 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 459 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 removed outlier: 3.567A pdb=" N GLU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.745A pdb=" N ALA D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 removed outlier: 3.610A pdb=" N LYS D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.817A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 247' Processing helix chain 'D' and resid 249 through 262 removed outlier: 3.945A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.579A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.522A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.142A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 412 removed outlier: 4.700A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ASP D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 431 Processing helix chain 'D' and resid 437 through 442 removed outlier: 4.216A pdb=" N VAL D 440 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR D 442 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.575A pdb=" N LEU D 460 " --> pdb=" O ARG D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 473 No H-bonds generated for 'chain 'D' and resid 471 through 473' Processing helix chain 'D' and resid 480 through 495 Processing helix chain 'E' and resid 11 through 24 removed outlier: 3.722A pdb=" N GLU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 176 through 185 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 233 through 251 Proline residue: E 240 - end of helix removed outlier: 3.855A pdb=" N PHE E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 277 Processing helix chain 'E' and resid 284 through 286 No H-bonds generated for 'chain 'E' and resid 284 through 286' Processing helix chain 'E' and resid 289 through 301 removed outlier: 4.107A pdb=" N PHE E 292 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER E 296 " --> pdb=" O TYR E 293 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG E 297 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 299 " --> pdb=" O SER E 296 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU E 300 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG E 301 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 336 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 374 through 394 removed outlier: 4.052A pdb=" N LYS E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 383 " --> pdb=" O VAL E 379 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 400 No H-bonds generated for 'chain 'E' and resid 397 through 400' Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.898A pdb=" N GLN E 410 " --> pdb=" O ALA E 406 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 442 Processing helix chain 'E' and resid 451 through 468 removed outlier: 4.633A pdb=" N ARG E 455 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LYS E 456 " --> pdb=" O ASP E 452 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 459 " --> pdb=" O ARG E 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 478 Processing helix chain 'E' and resid 484 through 502 removed outlier: 3.803A pdb=" N ALA E 493 " --> pdb=" O LEU E 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 178 through 192 removed outlier: 4.457A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 243 through 246 No H-bonds generated for 'chain 'F' and resid 243 through 246' Processing helix chain 'F' and resid 249 through 263 Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.680A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 313 removed outlier: 3.867A pdb=" N ARG F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 3.541A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 377 through 407 removed outlier: 7.564A pdb=" N GLU F 382 " --> pdb=" O ARG F 378 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N GLU F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS F 384 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 415 through 431 Processing helix chain 'F' and resid 437 through 442 removed outlier: 3.750A pdb=" N VAL F 440 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F 441 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR F 442 " --> pdb=" O GLU F 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 437 through 442' Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 473 No H-bonds generated for 'chain 'F' and resid 471 through 473' Processing helix chain 'F' and resid 480 through 492 removed outlier: 3.570A pdb=" N ASN F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 17 removed outlier: 4.446A pdb=" N SER A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.696A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 253 Proline residue: A 240 - end of helix removed outlier: 3.544A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.286A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 296 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 297 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.598A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.603A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.937A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 3.543A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 467 removed outlier: 3.883A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 484 through 503 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 275 through 286 removed outlier: 3.503A pdb=" N GLY B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 302 through 312 removed outlier: 3.513A pdb=" N GLY B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 337 through 345 removed outlier: 3.726A pdb=" N THR B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 382 through 408 removed outlier: 3.601A pdb=" N LYS B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.136A pdb=" N VAL B 440 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR B 442 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.522A pdb=" N ILE B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 480 through 495 Processing helix chain 'e' and resid 89 through 105 Processing helix chain 'e' and resid 109 through 129 removed outlier: 3.900A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR e 124 " --> pdb=" O ARG e 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG e 125 " --> pdb=" O ARG e 121 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL e 126 " --> pdb=" O ALA e 122 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 81 Processing helix chain 'g' and resid 83 through 100 Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.526A pdb=" N ARG g 144 " --> pdb=" O LYS g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 162 through 170 removed outlier: 3.589A pdb=" N ARG g 170 " --> pdb=" O THR g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 203 removed outlier: 3.615A pdb=" N ALA g 193 " --> pdb=" O LYS g 189 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix Processing helix chain 'S' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE S 22 " --> pdb=" O GLY S 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Proline residue: S 24 - end of helix removed outlier: 3.761A pdb=" N GLY S 29 " --> pdb=" O GLY S 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY S 47 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG S 50 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY S 51 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU S 57 " --> pdb=" O LEU S 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 62 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL S 69 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL S 70 " --> pdb=" O GLY S 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix removed outlier: 3.760A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY N 38 " --> pdb=" O GLN N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY N 47 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG N 50 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY N 51 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU N 57 " --> pdb=" O LEU N 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA N 62 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL N 69 " --> pdb=" O TYR N 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL N 70 " --> pdb=" O GLY N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 3.760A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY O 38 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY O 47 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG O 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY O 51 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU O 57 " --> pdb=" O LEU O 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA O 62 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL O 69 " --> pdb=" O TYR O 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL O 70 " --> pdb=" O GLY O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 3.760A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY P 47 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG P 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY P 51 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU P 57 " --> pdb=" O LEU P 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA P 62 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL P 69 " --> pdb=" O TYR P 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL P 70 " --> pdb=" O GLY P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix removed outlier: 3.760A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY Q 47 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY Q 51 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU Q 57 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA Q 62 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR Q 66 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL Q 69 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL Q 70 " --> pdb=" O GLY Q 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.761A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY R 47 " --> pdb=" O GLU R 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG R 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY R 51 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU R 57 " --> pdb=" O LEU R 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA R 62 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 69 " --> pdb=" O TYR R 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL R 70 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY M 23 " --> pdb=" O LEU M 19 " (cutoff:3.500A) Proline residue: M 24 - end of helix removed outlier: 3.760A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY M 38 " --> pdb=" O GLN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY M 47 " --> pdb=" O GLU M 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG M 50 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU M 57 " --> pdb=" O LEU M 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA M 62 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR M 66 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL M 69 " --> pdb=" O TYR M 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL M 70 " --> pdb=" O GLY M 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL T 17 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix removed outlier: 3.760A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY T 38 " --> pdb=" O GLN T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY T 47 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG T 50 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY T 51 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU T 54 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU T 57 " --> pdb=" O LEU T 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA T 62 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL T 69 " --> pdb=" O TYR T 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL T 70 " --> pdb=" O GLY T 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Proline residue: G 24 - end of helix removed outlier: 3.760A pdb=" N GLY G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY G 47 " --> pdb=" O GLU G 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 57 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA G 62 " --> pdb=" O PHE G 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 66 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 69 " --> pdb=" O TYR G 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL G 70 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Proline residue: H 24 - end of helix removed outlier: 3.760A pdb=" N GLY H 29 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 38 " --> pdb=" O GLN H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY H 47 " --> pdb=" O GLU H 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG H 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 51 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA H 62 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR H 66 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 69 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL H 70 " --> pdb=" O GLY H 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY L 23 " --> pdb=" O LEU L 19 " (cutoff:3.500A) Proline residue: L 24 - end of helix removed outlier: 3.760A pdb=" N GLY L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY L 38 " --> pdb=" O GLN L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 75 removed outlier: 4.740A pdb=" N GLY L 47 " --> pdb=" O GLU L 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG L 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY L 51 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L 57 " --> pdb=" O LEU L 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA L 62 " --> pdb=" O PHE L 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 69 " --> pdb=" O TYR L 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL L 70 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY K 23 " --> pdb=" O LEU K 19 " (cutoff:3.500A) Proline residue: K 24 - end of helix removed outlier: 3.759A pdb=" N GLY K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY K 47 " --> pdb=" O GLU K 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG K 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU K 54 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 57 " --> pdb=" O LEU K 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA K 62 " --> pdb=" O PHE K 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL K 69 " --> pdb=" O TYR K 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL K 70 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 41 removed outlier: 3.866A pdb=" N VAL J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY J 23 " --> pdb=" O LEU J 19 " (cutoff:3.500A) Proline residue: J 24 - end of helix removed outlier: 3.761A pdb=" N GLY J 29 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY J 38 " --> pdb=" O GLN J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY J 47 " --> pdb=" O GLU J 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG J 50 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY J 51 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 54 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 57 " --> pdb=" O LEU J 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA J 62 " --> pdb=" O PHE J 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR J 66 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL J 69 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL J 70 " --> pdb=" O GLY J 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 41 removed outlier: 3.867A pdb=" N VAL I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) Proline residue: I 24 - end of helix removed outlier: 3.761A pdb=" N GLY I 29 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY I 38 " --> pdb=" O GLN I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 75 removed outlier: 4.738A pdb=" N GLY I 47 " --> pdb=" O GLU I 44 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG I 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY I 51 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU I 54 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 57 " --> pdb=" O LEU I 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA I 62 " --> pdb=" O PHE I 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR I 66 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 69 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL I 70 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 201 removed outlier: 4.360A pdb=" N THR p 110 " --> pdb=" O LYS p 106 " (cutoff:3.500A) Proline residue: p 111 - end of helix Processing helix chain 'p' and resid 204 through 218 removed outlier: 3.769A pdb=" N ILE p 214 " --> pdb=" O LEU p 210 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL p 215 " --> pdb=" O SER p 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS p 216 " --> pdb=" O ASP p 212 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS p 217 " --> pdb=" O ASP p 213 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 158 removed outlier: 3.593A pdb=" N VAL b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL b 37 " --> pdb=" O ASN b 33 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN b 66 " --> pdb=" O ASN b 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL b 97 " --> pdb=" O ASP b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 181 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 106 removed outlier: 3.535A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE d 105 " --> pdb=" O LYS d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 Processing helix chain 'd' and resid 154 through 173 removed outlier: 5.283A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU d 160 " --> pdb=" O LEU d 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN d 170 " --> pdb=" O ASP d 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 248 removed outlier: 3.934A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'a' and resid 28 through 30 Processing sheet with id= B, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.537A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.702A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.530A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 315 through 318 removed outlier: 5.831A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 58 through 64 removed outlier: 4.636A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN D 19 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= H, first strand: chain 'D' and resid 348 through 350 removed outlier: 8.829A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE D 272 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.973A pdb=" N ILE E 61 " --> pdb=" O MET E 77 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY E 73 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU E 67 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS E 43 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL E 32 " --> pdb=" O HIS E 43 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.691A pdb=" N GLU E 126 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 341 through 345 Processing sheet with id= L, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.167A pdb=" N SER E 313 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE E 259 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR E 315 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU E 317 " --> pdb=" O TYR E 261 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 61 through 64 removed outlier: 4.152A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= O, first strand: chain 'F' and resid 348 through 351 Processing sheet with id= P, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.485A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.908A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.545A pdb=" N LEU A 167 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 313 through 318 Processing sheet with id= T, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.936A pdb=" N GLU B 90 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 75 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 68 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG B 73 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 23 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= V, first strand: chain 'B' and resid 348 through 351 removed outlier: 7.897A pdb=" N ILE B 168 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER B 323 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU B 170 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN B 325 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY B 172 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 327 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 268 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 324 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 270 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 326 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 272 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 328 " --> pdb=" O ILE B 272 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'e' and resid 4 through 8 removed outlier: 3.651A pdb=" N GLU e 73 " --> pdb=" O GLY e 70 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'e' and resid 31 through 34 removed outlier: 3.624A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU e 53 " --> pdb=" O GLN e 56 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'e' and resid 46 through 48 removed outlier: 3.513A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 155 through 160 removed outlier: 6.866A pdb=" N VAL g 118 " --> pdb=" O THR g 156 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE g 158 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU g 211 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL g 123 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU g 213 " --> pdb=" O VAL g 123 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'g' and resid 251 through 259 removed outlier: 4.180A pdb=" N ASP g 252 " --> pdb=" O ILE g 271 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.628A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) 2156 hydrogen bonds defined for protein. 5334 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: 14.13 Time building geometry restraints manager: 16.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.23: 2220 1.23 - 1.48: 20510 1.48 - 1.74: 16801 1.74 - 1.99: 246 1.99 - 2.25: 1 Bond restraints: 39778 Sorted by residual: bond pdb=" C GLN b 77 " pdb=" N LEU b 78 " ideal model delta sigma weight residual 1.335 2.248 -0.913 1.25e-02 6.40e+03 5.34e+03 bond pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 1.330 1.731 -0.401 1.39e-02 5.18e+03 8.34e+02 bond pdb=" C PHE D 276 " pdb=" N ARG D 277 " ideal model delta sigma weight residual 1.335 0.970 0.365 1.31e-02 5.83e+03 7.75e+02 bond pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 1.331 1.635 -0.304 1.38e-02 5.25e+03 4.86e+02 bond pdb=" C GLY A 30 " pdb=" N THR A 31 " ideal model delta sigma weight residual 1.331 1.579 -0.248 1.55e-02 4.16e+03 2.56e+02 ... (remaining 39773 not shown) Histogram of bond angle deviations from ideal: 81.12 - 95.84: 6 95.84 - 110.56: 12739 110.56 - 125.29: 40856 125.29 - 140.01: 341 140.01 - 154.73: 1 Bond angle restraints: 53943 Sorted by residual: angle pdb=" O GLY C 30 " pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 123.49 98.52 24.97 8.00e-01 1.56e+00 9.74e+02 angle pdb=" O GLY E 30 " pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 123.29 154.73 -31.44 1.06e+00 8.90e-01 8.80e+02 angle pdb=" C GLY E 30 " pdb=" N THR E 31 " pdb=" CA THR E 31 " ideal model delta sigma weight residual 122.74 85.10 37.64 1.54e+00 4.22e-01 5.97e+02 angle pdb=" CA GLY C 30 " pdb=" C GLY C 30 " pdb=" N THR C 31 " ideal model delta sigma weight residual 115.49 138.77 -23.28 1.03e+00 9.43e-01 5.11e+02 angle pdb=" CA GLY E 30 " pdb=" C GLY E 30 " pdb=" N THR E 31 " ideal model delta sigma weight residual 115.24 81.12 34.12 1.59e+00 3.96e-01 4.60e+02 ... (remaining 53938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 23525 26.83 - 53.67: 622 53.67 - 80.50: 60 80.50 - 107.34: 7 107.34 - 134.17: 4 Dihedral angle restraints: 24218 sinusoidal: 9463 harmonic: 14755 Sorted by residual: dihedral pdb=" CA ASP C 262 " pdb=" C ASP C 262 " pdb=" N ASP C 263 " pdb=" CA ASP C 263 " ideal model delta harmonic sigma weight residual -180.00 -49.94 -130.06 0 5.00e+00 4.00e-02 6.77e+02 dihedral pdb=" CA ASP A 262 " pdb=" C ASP A 262 " pdb=" N ASP A 263 " pdb=" CA ASP A 263 " ideal model delta harmonic sigma weight residual -180.00 -51.19 -128.81 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ASP E 262 " pdb=" C ASP E 262 " pdb=" N ASP E 263 " pdb=" CA ASP E 263 " ideal model delta harmonic sigma weight residual 0.00 -44.86 44.86 0 5.00e+00 4.00e-02 8.05e+01 ... (remaining 24215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5868 0.146 - 0.292: 498 0.292 - 0.438: 69 0.438 - 0.584: 6 0.584 - 0.730: 15 Chirality restraints: 6456 Sorted by residual: chirality pdb=" CB VAL T 81 " pdb=" CA VAL T 81 " pdb=" CG1 VAL T 81 " pdb=" CG2 VAL T 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB VAL M 81 " pdb=" CA VAL M 81 " pdb=" CG1 VAL M 81 " pdb=" CG2 VAL M 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CB VAL S 81 " pdb=" CA VAL S 81 " pdb=" CG1 VAL S 81 " pdb=" CG2 VAL S 81 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 6453 not shown) Planarity restraints: 6961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU b 181 " 0.067 2.00e-02 2.50e+03 1.24e-01 1.55e+02 pdb=" C GLU b 181 " -0.215 2.00e-02 2.50e+03 pdb=" O GLU b 181 " 0.080 2.00e-02 2.50e+03 pdb=" N ILE b 182 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 77 " -0.045 2.00e-02 2.50e+03 8.90e-02 7.92e+01 pdb=" C ALA Q 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA Q 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN Q 78 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 77 " -0.045 2.00e-02 2.50e+03 8.89e-02 7.91e+01 pdb=" C ALA M 77 " 0.154 2.00e-02 2.50e+03 pdb=" O ALA M 77 " -0.058 2.00e-02 2.50e+03 pdb=" N ASN M 78 " -0.052 2.00e-02 2.50e+03 ... (remaining 6958 not shown) Histogram of nonbonded interaction distances: 0.34 - 1.25: 114 1.25 - 2.17: 593 2.17 - 3.08: 31125 3.08 - 3.99: 106954 3.99 - 4.90: 203592 Warning: very small nonbonded interaction distances. Nonbonded interactions: 342378 Sorted by model distance: nonbonded pdb=" CB ALA a 54 " pdb=" CD1 TYR p 108 " model vdw 0.343 3.760 nonbonded pdb=" CA GLN a 121 " pdb=" C ASP b 25 " model vdw 0.416 3.700 nonbonded pdb=" CG1 VAL p 147 " pdb=" CB LEU b 85 " model vdw 0.438 3.860 nonbonded pdb=" CD GLN a 121 " pdb=" OD1 ASP b 25 " model vdw 0.482 3.270 nonbonded pdb=" CA ARG A 14 " pdb=" OD1 ASP p 213 " model vdw 0.484 3.470 ... (remaining 342373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 503) selection = (chain 'C' and resid 7 through 503) selection = (chain 'E' and resid 7 through 503) } ncs_group { reference = (chain 'B' and resid 18 through 494) selection = (chain 'D' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.030 Extract box with map and model: 11.270 Check model and map are aligned: 0.530 Set scattering table: 0.360 Process input model: 98.640 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.370 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: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 : 0.015 0.913 39778 Z= 1.017 Angle : 1.445 37.643 53943 Z= 0.963 Chirality : 0.094 0.730 6456 Planarity : 0.009 0.124 6961 Dihedral : 12.127 134.172 14763 Min Nonbonded Distance : 0.343 Molprobity Statistics. All-atom Clashscore : 62.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.04 % Rotamer: Outliers : 0.15 % Allowed : 5.46 % Favored : 94.40 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 5147 helix: 0.85 (0.10), residues: 2777 sheet: -1.33 (0.21), residues: 564 loop : -1.11 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP a 110 HIS 0.018 0.003 HIS E 295 PHE 0.067 0.003 PHE B 171 TYR 0.034 0.003 TYR E 287 ARG 0.022 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10294 Ramachandran restraints generated. 5147 Oldfield, 0 Emsley, 5147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1810 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 169 PRO cc_start: 0.0563 (Cg_exo) cc_final: 0.0341 (Cg_endo) REVERT: C 9 ILE cc_start: 0.8047 (tt) cc_final: 0.7685 (tt) REVERT: C 71 ASN cc_start: 0.8103 (p0) cc_final: 0.7824 (p0) REVERT: C 105 LEU cc_start: 0.8946 (mt) cc_final: 0.8341 (mt) REVERT: C 166 GLU cc_start: 0.9195 (tp30) cc_final: 0.8920 (tp30) REVERT: C 184 ILE cc_start: 0.9247 (mt) cc_final: 0.8938 (mm) REVERT: C 190 GLN cc_start: 0.7617 (mp10) cc_final: 0.7230 (mm-40) REVERT: C 258 LEU cc_start: 0.9205 (tp) cc_final: 0.8850 (tp) REVERT: C 274 MET cc_start: 0.8986 (mtm) cc_final: 0.8721 (mtm) REVERT: C 285 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7876 (tt0) REVERT: C 287 TYR cc_start: 0.8970 (m-80) cc_final: 0.8248 (m-10) REVERT: C 290 ASP cc_start: 0.8295 (m-30) cc_final: 0.7835 (t0) REVERT: C 365 SER cc_start: 0.9031 (t) cc_final: 0.8532 (m) REVERT: C 409 ASN cc_start: 0.7964 (m-40) cc_final: 0.7281 (m-40) REVERT: C 417 LEU cc_start: 0.9086 (mt) cc_final: 0.8483 (mm) REVERT: C 447 ASP cc_start: 0.7686 (m-30) cc_final: 0.7263 (p0) REVERT: C 451 LEU cc_start: 0.8289 (mt) cc_final: 0.7887 (mt) REVERT: C 460 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8711 (mt-10) REVERT: C 480 LYS cc_start: 0.8589 (mttt) cc_final: 0.8241 (ptmt) REVERT: C 498 MET cc_start: 0.8080 (ttm) cc_final: 0.7288 (tpt) REVERT: D 72 ASN cc_start: 0.8012 (m-40) cc_final: 0.7634 (m110) REVERT: D 193 HIS cc_start: 0.7194 (m-70) cc_final: 0.6863 (m90) REVERT: D 306 MET cc_start: 0.9160 (tpp) cc_final: 0.8736 (tpp) REVERT: D 333 ASP cc_start: 0.8399 (t0) cc_final: 0.7919 (t0) REVERT: D 454 THR cc_start: 0.8837 (m) cc_final: 0.8241 (m) REVERT: D 462 LEU cc_start: 0.8968 (mt) cc_final: 0.8686 (tt) REVERT: E 53 LEU cc_start: 0.9133 (mt) cc_final: 0.8811 (tt) REVERT: E 74 VAL cc_start: 0.8774 (t) cc_final: 0.8516 (p) REVERT: E 147 LEU cc_start: 0.8196 (tt) cc_final: 0.7816 (tt) REVERT: E 237 TYR cc_start: 0.8861 (t80) cc_final: 0.8413 (t80) REVERT: E 290 ASP cc_start: 0.9027 (m-30) cc_final: 0.8761 (t0) REVERT: E 292 PHE cc_start: 0.9173 (t80) cc_final: 0.8859 (t80) REVERT: E 298 LEU cc_start: 0.9293 (tp) cc_final: 0.9082 (tt) REVERT: E 342 GLN cc_start: 0.8997 (pm20) cc_final: 0.8787 (pm20) REVERT: E 445 TYR cc_start: 0.6112 (m-80) cc_final: 0.5723 (m-80) REVERT: E 456 LYS cc_start: 0.8579 (tttt) cc_final: 0.8351 (mmmt) REVERT: F 27 ILE cc_start: 0.9252 (mt) cc_final: 0.8991 (mp) REVERT: F 86 THR cc_start: 0.8707 (m) cc_final: 0.8367 (m) REVERT: F 158 LEU cc_start: 0.9617 (tp) cc_final: 0.9328 (tp) REVERT: F 196 VAL cc_start: 0.8488 (t) cc_final: 0.8047 (p) REVERT: F 239 MET cc_start: 0.8276 (mtt) cc_final: 0.7875 (mtt) REVERT: F 264 ASN cc_start: 0.8350 (m-40) cc_final: 0.7723 (t0) REVERT: F 311 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7890 (tp30) REVERT: F 369 ASP cc_start: 0.8081 (t0) cc_final: 0.7697 (t0) REVERT: F 442 THR cc_start: 0.8440 (p) cc_final: 0.8190 (t) REVERT: A 35 VAL cc_start: 0.8642 (t) cc_final: 0.7925 (p) REVERT: A 140 ARG cc_start: 0.8789 (mtt180) cc_final: 0.8405 (mtt-85) REVERT: A 154 ILE cc_start: 0.9381 (mp) cc_final: 0.9160 (mp) REVERT: A 155 ASP cc_start: 0.7085 (m-30) cc_final: 0.6685 (t0) REVERT: A 195 VAL cc_start: 0.9285 (t) cc_final: 0.9027 (t) REVERT: A 231 SER cc_start: 0.9531 (p) cc_final: 0.9064 (p) REVERT: A 264 LEU cc_start: 0.9440 (mt) cc_final: 0.9087 (mt) REVERT: A 266 LYS cc_start: 0.8669 (mttp) cc_final: 0.8323 (mmmm) REVERT: A 267 GLN cc_start: 0.8834 (tt0) cc_final: 0.8628 (tt0) REVERT: A 274 MET cc_start: 0.8454 (mtp) cc_final: 0.8225 (mmp) REVERT: A 340 ASP cc_start: 0.7744 (m-30) cc_final: 0.7541 (m-30) REVERT: B 44 TYR cc_start: 0.8689 (m-10) cc_final: 0.8392 (m-80) REVERT: B 79 MET cc_start: 0.9043 (mmm) cc_final: 0.8173 (mmm) REVERT: B 80 SER cc_start: 0.9288 (m) cc_final: 0.8880 (p) REVERT: B 199 PHE cc_start: 0.8077 (t80) cc_final: 0.7728 (t80) REVERT: B 239 MET cc_start: 0.8640 (mtt) cc_final: 0.8090 (mtt) REVERT: B 299 GLN cc_start: 0.9094 (pm20) cc_final: 0.8564 (pt0) REVERT: B 311 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 370 SER cc_start: 0.9359 (m) cc_final: 0.8806 (p) REVERT: B 390 ARG cc_start: 0.8597 (ttm170) cc_final: 0.7958 (mtp180) REVERT: B 423 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8555 (ttm110) REVERT: B 476 LEU cc_start: 0.8928 (mt) cc_final: 0.7800 (mt) REVERT: e 22 ILE cc_start: 0.8293 (pt) cc_final: 0.8090 (pt) REVERT: e 40 THR cc_start: 0.5406 (m) cc_final: 0.5098 (p) REVERT: e 111 GLN cc_start: 0.8684 (tt0) cc_final: 0.8380 (mp10) REVERT: g 135 ASN cc_start: 0.8498 (m-40) cc_final: 0.8143 (t0) REVERT: g 211 GLU cc_start: 0.7833 (pt0) cc_final: 0.7627 (pt0) REVERT: g 231 LEU cc_start: 0.8093 (mt) cc_final: 0.7522 (mt) REVERT: g 260 LYS cc_start: 0.7507 (tttt) cc_final: 0.7211 (pttm) REVERT: g 285 GLU cc_start: 0.8336 (tp30) cc_final: 0.7489 (tm-30) REVERT: g 287 ASP cc_start: 0.8327 (t70) cc_final: 0.7690 (m-30) REVERT: g 304 ILE cc_start: 0.8448 (mt) cc_final: 0.8220 (mm) REVERT: S 28 GLN cc_start: 0.6056 (mt0) cc_final: 0.5391 (tt0) REVERT: S 34 GLN cc_start: 0.6999 (tt0) cc_final: 0.6622 (tt0) REVERT: S 60 MET cc_start: 0.5830 (mtm) cc_final: 0.5110 (mmm) REVERT: N 34 GLN cc_start: 0.7649 (tt0) cc_final: 0.6925 (tt0) REVERT: Q 34 GLN cc_start: 0.7175 (tt0) cc_final: 0.6751 (tt0) REVERT: Q 60 MET cc_start: 0.4439 (mtm) cc_final: 0.3836 (mtp) REVERT: G 34 GLN cc_start: 0.5396 (tt0) cc_final: 0.4781 (tt0) REVERT: L 50 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6791 (mtp180) REVERT: K 68 LEU cc_start: 0.6245 (tp) cc_final: 0.5734 (tp) REVERT: K 79 PRO cc_start: 0.2309 (Cg_endo) cc_final: 0.1883 (Cg_exo) REVERT: J 28 GLN cc_start: 0.7706 (mt0) cc_final: 0.6054 (mm110) REVERT: J 52 THR cc_start: 0.7391 (m) cc_final: 0.7157 (p) REVERT: I 46 GLU cc_start: 0.2182 (tt0) cc_final: 0.1724 (tm-30) REVERT: p 191 SER cc_start: 0.7520 (p) cc_final: 0.7191 (t) REVERT: d 92 LEU cc_start: 0.8374 (mt) cc_final: 0.7893 (mt) REVERT: d 138 LEU cc_start: 0.7302 (mt) cc_final: 0.6900 (mt) REVERT: d 151 ASP cc_start: 0.8161 (t0) cc_final: 0.7898 (m-30) REVERT: d 157 LEU cc_start: 0.8777 (pp) cc_final: 0.8389 (pp) REVERT: d 221 PHE cc_start: 0.7879 (p90) cc_final: 0.7630 (p90) REVERT: d 244 ILE cc_start: 0.7942 (mt) cc_final: 0.7575 (mt) outliers start: 6 outliers final: 1 residues processed: 1812 average time/residue: 0.5609 time to fit residues: 1617.3791 Evaluate side-chains 924 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 923 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 424 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 211 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 257 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 456 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 398 GLN ** C 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN E 66 ASN E 148 GLN E 187 GLN E 214 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN F 112 ASN F 193 HIS F 210 ASN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS F 376 GLN ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 351 ASN A 398 GLN A 423 GLN A 495 GLN B 45 ASN B 133 HIS B 193 HIS B 210 ASN B 238 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN g 76 GLN g 81 ASN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN S 28 GLN O 42 GLN ** T 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 206 GLN ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 GLN d 124 ASN d 141 HIS d 147 ASN ** d 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.198 39778 Z= 0.386 Angle : 0.916 33.264 53943 Z= 0.474 Chirality : 0.052 0.440 6456 Planarity : 0.007 0.099 6961 Dihedral : 7.600 113.125 5682 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.84 % Favored : 97.05 % Rotamer: Outliers : 0.68 % Allowed : 5.28 % Favored : 94.03 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5149 helix: 0.43 (0.09), residues: 2783 sheet: -0.82 (0.20), residues: 601 loop : -0.77 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP e 57 HIS 0.013 0.002 HIS a 124 PHE 0.045 0.003 PHE a 72 TYR 0.040 0.002 TYR a 74 ARG 0.011 0.001 ARG p 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1173 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.1433 (tt) cc_final: 0.1159 (mt) REVERT: a 144 THR cc_start: 0.8619 (p) cc_final: 0.8401 (p) REVERT: C 71 ASN cc_start: 0.8756 (p0) cc_final: 0.8411 (p0) REVERT: C 130 ILE cc_start: 0.8974 (mt) cc_final: 0.8592 (mt) REVERT: C 184 ILE cc_start: 0.9078 (mt) cc_final: 0.8837 (mm) REVERT: C 194 CYS cc_start: 0.8941 (m) cc_final: 0.8740 (m) REVERT: C 197 VAL cc_start: 0.9225 (t) cc_final: 0.9007 (p) REVERT: C 215 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 290 ASP cc_start: 0.8352 (m-30) cc_final: 0.7948 (t0) REVERT: C 365 SER cc_start: 0.8908 (t) cc_final: 0.8531 (m) REVERT: C 384 LYS cc_start: 0.8695 (mttt) cc_final: 0.7588 (tptm) REVERT: C 458 LEU cc_start: 0.9497 (mm) cc_final: 0.9288 (mm) REVERT: C 480 LYS cc_start: 0.8808 (mttt) cc_final: 0.8383 (ptmt) REVERT: C 498 MET cc_start: 0.8122 (ttm) cc_final: 0.7114 (tpt) REVERT: D 280 GLN cc_start: 0.8582 (pp30) cc_final: 0.8349 (pp30) REVERT: D 351 VAL cc_start: 0.9047 (t) cc_final: 0.8723 (p) REVERT: D 475 TYR cc_start: 0.7479 (t80) cc_final: 0.7130 (t80) REVERT: D 476 LEU cc_start: 0.9385 (mt) cc_final: 0.8614 (pp) REVERT: D 481 ASP cc_start: 0.8951 (m-30) cc_final: 0.8557 (p0) REVERT: E 53 LEU cc_start: 0.9274 (mt) cc_final: 0.8938 (mp) REVERT: E 66 ASN cc_start: 0.8668 (m-40) cc_final: 0.8398 (t0) REVERT: E 191 ASN cc_start: 0.8406 (m-40) cc_final: 0.7831 (p0) REVERT: E 251 MET cc_start: 0.8525 (ttt) cc_final: 0.7420 (tpp) REVERT: E 258 LEU cc_start: 0.9317 (tp) cc_final: 0.9008 (tp) REVERT: E 342 GLN cc_start: 0.8788 (pm20) cc_final: 0.7427 (pt0) REVERT: E 456 LYS cc_start: 0.8683 (tttt) cc_final: 0.8262 (mmmt) REVERT: E 497 GLN cc_start: 0.6406 (tp40) cc_final: 0.5877 (tp40) REVERT: F 147 SER cc_start: 0.9050 (m) cc_final: 0.8782 (t) REVERT: F 158 LEU cc_start: 0.9714 (tp) cc_final: 0.9482 (tp) REVERT: F 183 MET cc_start: 0.8455 (mmm) cc_final: 0.8192 (mmp) REVERT: F 184 GLU cc_start: 0.8575 (tp30) cc_final: 0.8141 (tp30) REVERT: F 216 MET cc_start: 0.8525 (mmm) cc_final: 0.7931 (mpp) REVERT: F 292 MET cc_start: 0.8783 (mtt) cc_final: 0.8472 (mtt) REVERT: F 314 THR cc_start: 0.8794 (p) cc_final: 0.8553 (p) REVERT: F 374 MET cc_start: 0.8737 (mmm) cc_final: 0.8524 (mmt) REVERT: F 389 GLN cc_start: 0.7349 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 41 ARG cc_start: 0.8103 (mmt180) cc_final: 0.7804 (mmm160) REVERT: A 151 LEU cc_start: 0.8402 (mt) cc_final: 0.7913 (mp) REVERT: A 157 MET cc_start: 0.8966 (mpp) cc_final: 0.7913 (mpp) REVERT: A 195 VAL cc_start: 0.9397 (t) cc_final: 0.9132 (t) REVERT: A 219 MET cc_start: 0.8045 (tpp) cc_final: 0.7732 (tpt) REVERT: A 264 LEU cc_start: 0.9258 (mt) cc_final: 0.9032 (mt) REVERT: A 267 GLN cc_start: 0.9296 (tt0) cc_final: 0.8959 (tt0) REVERT: A 274 MET cc_start: 0.8538 (mtp) cc_final: 0.8202 (mtm) REVERT: A 290 ASP cc_start: 0.7869 (p0) cc_final: 0.7114 (p0) REVERT: A 335 VAL cc_start: 0.9783 (t) cc_final: 0.9494 (p) REVERT: A 344 PHE cc_start: 0.8299 (m-80) cc_final: 0.8056 (m-80) REVERT: A 382 LYS cc_start: 0.8731 (mttt) cc_final: 0.8103 (pttm) REVERT: A 436 MET cc_start: 0.8256 (ppp) cc_final: 0.7574 (tmm) REVERT: A 490 LEU cc_start: 0.9344 (tp) cc_final: 0.9048 (tp) REVERT: B 72 ASN cc_start: 0.8580 (m-40) cc_final: 0.8254 (m-40) REVERT: B 79 MET cc_start: 0.8753 (mmm) cc_final: 0.8302 (mmm) REVERT: B 80 SER cc_start: 0.9343 (m) cc_final: 0.9024 (p) REVERT: B 176 VAL cc_start: 0.9445 (m) cc_final: 0.9215 (p) REVERT: B 239 MET cc_start: 0.8524 (mtt) cc_final: 0.7997 (mtm) REVERT: B 241 GLU cc_start: 0.8601 (mp0) cc_final: 0.8237 (mp0) REVERT: B 251 LEU cc_start: 0.9441 (mt) cc_final: 0.9208 (mt) REVERT: B 370 SER cc_start: 0.9495 (m) cc_final: 0.9007 (p) REVERT: B 393 GLU cc_start: 0.8570 (pt0) cc_final: 0.8337 (pt0) REVERT: B 405 ILE cc_start: 0.9239 (pt) cc_final: 0.8907 (mt) REVERT: B 420 THR cc_start: 0.9184 (m) cc_final: 0.8907 (p) REVERT: B 435 PHE cc_start: 0.8426 (m-80) cc_final: 0.7747 (m-80) REVERT: B 476 LEU cc_start: 0.8898 (mt) cc_final: 0.8565 (mm) REVERT: B 492 MET cc_start: 0.8548 (mtm) cc_final: 0.8235 (ptp) REVERT: e 111 GLN cc_start: 0.8813 (tt0) cc_final: 0.8275 (mp10) REVERT: g 50 ARG cc_start: 0.8573 (tpt-90) cc_final: 0.8235 (tpt-90) REVERT: g 85 PHE cc_start: 0.8067 (t80) cc_final: 0.7074 (t80) REVERT: g 135 ASN cc_start: 0.8646 (m-40) cc_final: 0.8165 (t0) REVERT: g 136 MET cc_start: 0.8353 (tpp) cc_final: 0.7825 (tpp) REVERT: g 216 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8350 (ptpp) REVERT: g 282 LEU cc_start: 0.7347 (tp) cc_final: 0.7064 (pp) REVERT: g 284 PHE cc_start: 0.7510 (m-10) cc_final: 0.7206 (m-10) REVERT: g 287 ASP cc_start: 0.8199 (t70) cc_final: 0.7898 (t70) REVERT: S 28 GLN cc_start: 0.6570 (mt0) cc_final: 0.4972 (tt0) REVERT: S 60 MET cc_start: 0.6266 (mtm) cc_final: 0.5188 (mmm) REVERT: S 75 LEU cc_start: 0.7439 (tp) cc_final: 0.7126 (tp) REVERT: P 57 LEU cc_start: 0.4833 (mt) cc_final: 0.4477 (mt) REVERT: R 34 GLN cc_start: 0.7432 (mm110) cc_final: 0.6860 (mm110) REVERT: T 37 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7980 (mt-10) REVERT: I 50 ARG cc_start: 0.7876 (ttp80) cc_final: 0.6605 (ptp90) REVERT: p 83 LEU cc_start: 0.1985 (pp) cc_final: 0.0982 (pp) REVERT: b 66 ASN cc_start: 0.4125 (OUTLIER) cc_final: 0.3002 (t0) REVERT: d 155 ILE cc_start: 0.9049 (tt) cc_final: 0.8617 (mp) REVERT: d 157 LEU cc_start: 0.9146 (pp) cc_final: 0.8332 (pp) REVERT: d 189 ASP cc_start: 0.7589 (p0) cc_final: 0.7285 (p0) REVERT: d 223 ILE cc_start: 0.8675 (pt) cc_final: 0.8427 (tp) REVERT: d 224 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7920 (mtt-85) REVERT: d 247 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5420 (tt0) outliers start: 28 outliers final: 6 residues processed: 1194 average time/residue: 0.4961 time to fit residues: 972.9222 Evaluate side-chains 781 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 773 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 253 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 380 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 457 optimal weight: 4.9990 chunk 494 optimal weight: 3.9990 chunk 407 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 164 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN E 214 GLN ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN O 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN G 28 GLN p 143 GLN b 23 ASN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN d 141 HIS d 147 ASN d 247 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 39778 Z= 0.304 Angle : 0.744 15.907 53943 Z= 0.379 Chirality : 0.047 0.423 6456 Planarity : 0.005 0.069 6961 Dihedral : 6.983 110.554 5682 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5149 helix: 0.48 (0.10), residues: 2837 sheet: -0.72 (0.20), residues: 616 loop : -0.76 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 15 HIS 0.009 0.002 HIS e 37 PHE 0.037 0.002 PHE a 72 TYR 0.030 0.002 TYR a 74 ARG 0.008 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1009 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.1202 (tt) cc_final: 0.0766 (mt) REVERT: a 222 PHE cc_start: 0.7909 (t80) cc_final: 0.7359 (t80) REVERT: C 184 ILE cc_start: 0.9404 (mt) cc_final: 0.9073 (mm) REVERT: C 194 CYS cc_start: 0.8941 (m) cc_final: 0.8375 (m) REVERT: C 201 GLN cc_start: 0.7276 (mp10) cc_final: 0.6805 (mp10) REVERT: C 251 MET cc_start: 0.8187 (ttp) cc_final: 0.7911 (ttp) REVERT: C 258 LEU cc_start: 0.9473 (tp) cc_final: 0.9221 (tp) REVERT: C 274 MET cc_start: 0.8612 (mtm) cc_final: 0.8344 (mtt) REVERT: C 290 ASP cc_start: 0.8482 (m-30) cc_final: 0.8026 (t0) REVERT: C 365 SER cc_start: 0.8889 (t) cc_final: 0.8553 (m) REVERT: C 384 LYS cc_start: 0.8735 (mttt) cc_final: 0.8079 (tptm) REVERT: C 409 ASN cc_start: 0.7806 (m-40) cc_final: 0.7558 (m-40) REVERT: C 417 LEU cc_start: 0.9327 (mt) cc_final: 0.9115 (mt) REVERT: C 480 LYS cc_start: 0.8817 (mttt) cc_final: 0.8407 (ptmt) REVERT: C 498 MET cc_start: 0.7900 (ttm) cc_final: 0.6987 (tpt) REVERT: D 90 GLU cc_start: 0.7857 (pm20) cc_final: 0.7614 (pm20) REVERT: D 280 GLN cc_start: 0.8618 (pp30) cc_final: 0.8376 (pp30) REVERT: D 333 ASP cc_start: 0.9130 (t0) cc_final: 0.7497 (t0) REVERT: D 351 VAL cc_start: 0.9036 (t) cc_final: 0.8752 (p) REVERT: D 428 GLU cc_start: 0.8582 (pt0) cc_final: 0.8170 (pt0) REVERT: D 475 TYR cc_start: 0.7588 (t80) cc_final: 0.7193 (t80) REVERT: D 476 LEU cc_start: 0.9470 (mt) cc_final: 0.8729 (pp) REVERT: D 481 ASP cc_start: 0.8942 (m-30) cc_final: 0.8500 (p0) REVERT: D 492 MET cc_start: 0.8341 (tmm) cc_final: 0.8103 (tmm) REVERT: E 22 ARG cc_start: 0.6569 (mpp80) cc_final: 0.5870 (mpp80) REVERT: E 53 LEU cc_start: 0.9198 (mt) cc_final: 0.8557 (tt) REVERT: E 66 ASN cc_start: 0.8861 (m-40) cc_final: 0.8430 (t0) REVERT: E 191 ASN cc_start: 0.8461 (m-40) cc_final: 0.7929 (p0) REVERT: E 258 LEU cc_start: 0.9379 (tp) cc_final: 0.9067 (tp) REVERT: E 342 GLN cc_start: 0.8839 (pm20) cc_final: 0.7596 (pt0) REVERT: E 452 ASP cc_start: 0.8240 (m-30) cc_final: 0.7974 (t70) REVERT: E 456 LYS cc_start: 0.8680 (tttt) cc_final: 0.8279 (mmmt) REVERT: F 79 MET cc_start: 0.9101 (mmp) cc_final: 0.8863 (mmp) REVERT: F 89 MET cc_start: 0.8363 (ttt) cc_final: 0.8117 (ttt) REVERT: F 112 ASN cc_start: 0.8645 (m110) cc_final: 0.8250 (m110) REVERT: F 158 LEU cc_start: 0.9666 (tp) cc_final: 0.9402 (tp) REVERT: F 184 GLU cc_start: 0.8586 (tp30) cc_final: 0.8356 (tp30) REVERT: F 216 MET cc_start: 0.8547 (mmm) cc_final: 0.8090 (mpp) REVERT: F 241 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8085 (mm-30) REVERT: F 292 MET cc_start: 0.8950 (mtt) cc_final: 0.8575 (mtt) REVERT: F 314 THR cc_start: 0.8714 (p) cc_final: 0.8409 (p) REVERT: A 16 ARG cc_start: 0.6577 (mtm110) cc_final: 0.5347 (tpp-160) REVERT: A 41 ARG cc_start: 0.8013 (mmt180) cc_final: 0.7778 (mmm160) REVERT: A 52 GLU cc_start: 0.8888 (tt0) cc_final: 0.8185 (tt0) REVERT: A 157 MET cc_start: 0.8946 (mpp) cc_final: 0.8196 (mpp) REVERT: A 208 GLN cc_start: 0.9011 (tp40) cc_final: 0.8685 (mm-40) REVERT: A 267 GLN cc_start: 0.9252 (tt0) cc_final: 0.9041 (tt0) REVERT: A 290 ASP cc_start: 0.8036 (p0) cc_final: 0.7720 (p0) REVERT: A 382 LYS cc_start: 0.8662 (mttt) cc_final: 0.8097 (mmmm) REVERT: B 79 MET cc_start: 0.8957 (mmm) cc_final: 0.8299 (mmm) REVERT: B 80 SER cc_start: 0.9445 (m) cc_final: 0.9068 (p) REVERT: B 213 TYR cc_start: 0.8100 (t80) cc_final: 0.7782 (t80) REVERT: B 239 MET cc_start: 0.8438 (mtt) cc_final: 0.8068 (mtt) REVERT: B 298 TYR cc_start: 0.8624 (m-80) cc_final: 0.8245 (m-80) REVERT: B 370 SER cc_start: 0.9590 (m) cc_final: 0.9150 (p) REVERT: B 393 GLU cc_start: 0.8645 (pt0) cc_final: 0.8271 (pt0) REVERT: B 405 ILE cc_start: 0.9230 (pt) cc_final: 0.8977 (mt) REVERT: B 417 ASP cc_start: 0.8986 (m-30) cc_final: 0.8643 (m-30) REVERT: B 435 PHE cc_start: 0.8506 (m-80) cc_final: 0.7771 (m-80) REVERT: B 475 TYR cc_start: 0.9115 (t80) cc_final: 0.8583 (t80) REVERT: B 476 LEU cc_start: 0.8812 (mt) cc_final: 0.8015 (mt) REVERT: B 492 MET cc_start: 0.8489 (mtm) cc_final: 0.8160 (mtm) REVERT: e 40 THR cc_start: 0.4730 (m) cc_final: 0.4525 (m) REVERT: e 94 GLN cc_start: 0.9200 (tt0) cc_final: 0.8653 (mt0) REVERT: e 111 GLN cc_start: 0.8846 (tt0) cc_final: 0.8316 (mp10) REVERT: g 135 ASN cc_start: 0.8697 (m-40) cc_final: 0.8254 (t0) REVERT: g 136 MET cc_start: 0.8324 (tpp) cc_final: 0.7852 (tpp) REVERT: g 173 GLU cc_start: 0.7921 (pp20) cc_final: 0.7650 (pp20) REVERT: g 216 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8360 (ptpp) REVERT: g 282 LEU cc_start: 0.7235 (tp) cc_final: 0.7017 (pp) REVERT: g 287 ASP cc_start: 0.8236 (t70) cc_final: 0.7886 (t70) REVERT: S 28 GLN cc_start: 0.6413 (mt0) cc_final: 0.4735 (tt0) REVERT: S 60 MET cc_start: 0.6338 (mtm) cc_final: 0.5060 (mmm) REVERT: S 61 GLU cc_start: 0.5463 (mm-30) cc_final: 0.5107 (mm-30) REVERT: S 63 LEU cc_start: 0.5777 (mt) cc_final: 0.5355 (mt) REVERT: P 26 VAL cc_start: 0.6650 (m) cc_final: 0.6357 (p) REVERT: R 34 GLN cc_start: 0.8212 (mm110) cc_final: 0.7949 (mm110) REVERT: R 57 LEU cc_start: 0.5962 (pp) cc_final: 0.5721 (pp) REVERT: G 60 MET cc_start: 0.4265 (ttt) cc_final: 0.3995 (ttm) REVERT: H 49 ILE cc_start: 0.7632 (mt) cc_final: 0.7416 (mt) REVERT: J 28 GLN cc_start: 0.7272 (mt0) cc_final: 0.5898 (tt0) REVERT: J 60 MET cc_start: 0.7410 (mtt) cc_final: 0.6915 (mtp) REVERT: I 53 LEU cc_start: 0.6364 (tp) cc_final: 0.6113 (tp) REVERT: I 60 MET cc_start: 0.3886 (mtp) cc_final: 0.3557 (mtp) REVERT: p 83 LEU cc_start: 0.1685 (pp) cc_final: -0.0722 (pp) REVERT: p 152 ARG cc_start: 0.5491 (tpt170) cc_final: 0.5221 (mmp-170) REVERT: p 170 VAL cc_start: 0.5424 (t) cc_final: 0.5010 (p) REVERT: b 59 ARG cc_start: 0.6577 (mtm110) cc_final: 0.5996 (ttp80) REVERT: b 60 ILE cc_start: 0.3826 (tt) cc_final: 0.3536 (mm) REVERT: b 65 ARG cc_start: 0.5515 (ppt170) cc_final: 0.5246 (ptm-80) REVERT: b 179 MET cc_start: 0.4885 (ptm) cc_final: 0.4511 (ttp) REVERT: d 188 ASN cc_start: 0.7399 (m-40) cc_final: 0.7034 (m-40) REVERT: d 189 ASP cc_start: 0.7550 (p0) cc_final: 0.7302 (p0) REVERT: d 223 ILE cc_start: 0.8535 (pt) cc_final: 0.8243 (tp) REVERT: d 241 LEU cc_start: 0.9201 (tp) cc_final: 0.8943 (mt) outliers start: 8 outliers final: 1 residues processed: 1017 average time/residue: 0.5001 time to fit residues: 836.2952 Evaluate side-chains 725 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 452 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 307 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 486 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 435 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 ASN ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN B 71 ASN B 210 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 ASN p 206 GLN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39778 Z= 0.278 Angle : 0.702 12.177 53943 Z= 0.357 Chirality : 0.045 0.493 6456 Planarity : 0.005 0.070 6961 Dihedral : 6.574 105.404 5682 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5149 helix: 0.47 (0.10), residues: 2854 sheet: -0.64 (0.20), residues: 613 loop : -0.62 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 15 HIS 0.010 0.001 HIS e 37 PHE 0.034 0.002 PHE b 95 TYR 0.027 0.002 TYR B 259 ARG 0.010 0.001 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 970 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.1020 (tt) cc_final: 0.0583 (mt) REVERT: a 84 LYS cc_start: 0.7905 (tttt) cc_final: 0.7573 (mtpp) REVERT: a 165 ILE cc_start: 0.4089 (OUTLIER) cc_final: 0.3303 (pt) REVERT: C 184 ILE cc_start: 0.9329 (mt) cc_final: 0.9058 (mm) REVERT: C 194 CYS cc_start: 0.8986 (m) cc_final: 0.8637 (m) REVERT: C 274 MET cc_start: 0.8608 (mtm) cc_final: 0.8383 (mtt) REVERT: C 290 ASP cc_start: 0.8408 (m-30) cc_final: 0.7982 (t0) REVERT: C 384 LYS cc_start: 0.8668 (mttt) cc_final: 0.8081 (tptm) REVERT: C 409 ASN cc_start: 0.7910 (m-40) cc_final: 0.7639 (m-40) REVERT: C 480 LYS cc_start: 0.8845 (mttt) cc_final: 0.8422 (ptmt) REVERT: C 498 MET cc_start: 0.7945 (ttm) cc_final: 0.7068 (tpt) REVERT: D 90 GLU cc_start: 0.7796 (pm20) cc_final: 0.7488 (pm20) REVERT: D 183 MET cc_start: 0.9248 (mmm) cc_final: 0.8451 (mtt) REVERT: D 184 GLU cc_start: 0.8497 (tp30) cc_final: 0.8289 (tp30) REVERT: D 280 GLN cc_start: 0.8806 (pp30) cc_final: 0.8303 (pp30) REVERT: D 351 VAL cc_start: 0.9085 (t) cc_final: 0.8829 (p) REVERT: D 428 GLU cc_start: 0.8592 (pt0) cc_final: 0.8229 (pt0) REVERT: D 475 TYR cc_start: 0.7694 (t80) cc_final: 0.7255 (t80) REVERT: D 476 LEU cc_start: 0.9429 (mt) cc_final: 0.8774 (pp) REVERT: D 481 ASP cc_start: 0.8942 (m-30) cc_final: 0.8437 (p0) REVERT: D 492 MET cc_start: 0.8393 (tmm) cc_final: 0.8131 (tmm) REVERT: E 66 ASN cc_start: 0.8915 (m-40) cc_final: 0.8539 (t0) REVERT: E 157 MET cc_start: 0.7463 (mpp) cc_final: 0.7187 (mpp) REVERT: E 191 ASN cc_start: 0.8435 (m-40) cc_final: 0.8058 (p0) REVERT: E 251 MET cc_start: 0.8439 (ttt) cc_final: 0.7574 (tpp) REVERT: E 258 LEU cc_start: 0.9435 (tp) cc_final: 0.9169 (tp) REVERT: E 340 ASP cc_start: 0.8425 (m-30) cc_final: 0.8020 (m-30) REVERT: E 366 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7649 (ttm-80) REVERT: E 376 MET cc_start: 0.7536 (mmt) cc_final: 0.6754 (mmt) REVERT: E 436 MET cc_start: 0.7373 (ppp) cc_final: 0.7152 (ppp) REVERT: E 452 ASP cc_start: 0.8271 (m-30) cc_final: 0.7938 (t70) REVERT: E 456 LYS cc_start: 0.8644 (tttt) cc_final: 0.8203 (mmmt) REVERT: E 497 GLN cc_start: 0.6313 (tp40) cc_final: 0.6000 (tp40) REVERT: F 59 MET cc_start: 0.6429 (tpp) cc_final: 0.6045 (tmm) REVERT: F 112 ASN cc_start: 0.8654 (m110) cc_final: 0.7984 (m110) REVERT: F 116 GLU cc_start: 0.8537 (pm20) cc_final: 0.7858 (pm20) REVERT: F 184 GLU cc_start: 0.8579 (tp30) cc_final: 0.8332 (tp30) REVERT: F 208 GLU cc_start: 0.7951 (pp20) cc_final: 0.7586 (tm-30) REVERT: F 216 MET cc_start: 0.8383 (mmm) cc_final: 0.8103 (mpp) REVERT: F 239 MET cc_start: 0.8270 (mtm) cc_final: 0.7960 (mtm) REVERT: F 241 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7968 (mm-30) REVERT: F 292 MET cc_start: 0.9007 (mtt) cc_final: 0.8645 (mtt) REVERT: F 314 THR cc_start: 0.8807 (p) cc_final: 0.8564 (p) REVERT: F 374 MET cc_start: 0.8503 (mmt) cc_final: 0.8168 (mtp) REVERT: A 25 LYS cc_start: 0.8347 (tppt) cc_final: 0.8097 (tppt) REVERT: A 140 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8153 (mtt-85) REVERT: A 157 MET cc_start: 0.8863 (mpp) cc_final: 0.8216 (mpp) REVERT: A 219 MET cc_start: 0.8427 (tpp) cc_final: 0.8115 (tpp) REVERT: A 267 GLN cc_start: 0.9283 (tt0) cc_final: 0.9046 (tt0) REVERT: A 290 ASP cc_start: 0.8054 (p0) cc_final: 0.7372 (p0) REVERT: A 382 LYS cc_start: 0.8740 (mttt) cc_final: 0.7962 (pttm) REVERT: B 75 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7349 (mmt180) REVERT: B 79 MET cc_start: 0.8785 (mmm) cc_final: 0.8323 (mmm) REVERT: B 80 SER cc_start: 0.9444 (m) cc_final: 0.9141 (p) REVERT: B 167 LYS cc_start: 0.9043 (mppt) cc_final: 0.8652 (mppt) REVERT: B 168 ILE cc_start: 0.9611 (mm) cc_final: 0.9308 (mm) REVERT: B 213 TYR cc_start: 0.8142 (t80) cc_final: 0.7737 (t80) REVERT: B 241 GLU cc_start: 0.8705 (mp0) cc_final: 0.8381 (mp0) REVERT: B 298 TYR cc_start: 0.8437 (m-80) cc_final: 0.8104 (m-80) REVERT: B 370 SER cc_start: 0.9634 (m) cc_final: 0.9259 (p) REVERT: B 393 GLU cc_start: 0.8570 (pt0) cc_final: 0.8297 (pt0) REVERT: B 405 ILE cc_start: 0.9263 (pt) cc_final: 0.8963 (mt) REVERT: B 435 PHE cc_start: 0.8708 (m-80) cc_final: 0.7917 (m-80) REVERT: B 475 TYR cc_start: 0.9086 (t80) cc_final: 0.8544 (t80) REVERT: B 476 LEU cc_start: 0.8810 (mt) cc_final: 0.7942 (mt) REVERT: B 492 MET cc_start: 0.8397 (mtm) cc_final: 0.8060 (ptp) REVERT: e 94 GLN cc_start: 0.9076 (tt0) cc_final: 0.8640 (mt0) REVERT: e 111 GLN cc_start: 0.8776 (tt0) cc_final: 0.8300 (mp10) REVERT: e 112 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7749 (pttp) REVERT: e 114 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6432 (mp0) REVERT: g 135 ASN cc_start: 0.8709 (m-40) cc_final: 0.8290 (t0) REVERT: g 136 MET cc_start: 0.8338 (tpp) cc_final: 0.7855 (tpp) REVERT: g 173 GLU cc_start: 0.7938 (pp20) cc_final: 0.7578 (tm-30) REVERT: g 287 ASP cc_start: 0.8326 (t70) cc_final: 0.7976 (t0) REVERT: g 315 GLU cc_start: 0.8754 (tt0) cc_final: 0.8284 (tm-30) REVERT: g 323 MET cc_start: 0.8695 (mmp) cc_final: 0.8411 (mmm) REVERT: S 60 MET cc_start: 0.6548 (mtm) cc_final: 0.5468 (mmm) REVERT: S 63 LEU cc_start: 0.5484 (mt) cc_final: 0.5057 (mt) REVERT: S 74 LEU cc_start: 0.3886 (mm) cc_final: 0.3578 (mp) REVERT: O 30 THR cc_start: 0.6072 (p) cc_final: 0.5703 (p) REVERT: P 26 VAL cc_start: 0.6727 (m) cc_final: 0.6433 (p) REVERT: P 57 LEU cc_start: 0.5077 (mt) cc_final: 0.3913 (mt) REVERT: T 37 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8305 (mt-10) REVERT: G 34 GLN cc_start: 0.6306 (tt0) cc_final: 0.5426 (tt0) REVERT: G 60 MET cc_start: 0.4544 (ttt) cc_final: 0.3968 (ttt) REVERT: J 28 GLN cc_start: 0.6347 (mt0) cc_final: 0.5725 (tt0) REVERT: J 60 MET cc_start: 0.7376 (mtt) cc_final: 0.7049 (mtp) REVERT: p 83 LEU cc_start: 0.2734 (pp) cc_final: 0.1608 (pp) REVERT: p 102 PHE cc_start: 0.2773 (m-80) cc_final: 0.2147 (m-80) REVERT: p 116 MET cc_start: 0.4795 (mmt) cc_final: 0.4030 (mmt) REVERT: p 152 ARG cc_start: 0.5883 (tpt170) cc_final: 0.5480 (mmp-170) REVERT: d 72 ASP cc_start: 0.7619 (t0) cc_final: 0.7336 (t0) REVERT: d 88 VAL cc_start: 0.8200 (t) cc_final: 0.7908 (m) REVERT: d 188 ASN cc_start: 0.7532 (m-40) cc_final: 0.7253 (m-40) REVERT: d 241 LEU cc_start: 0.9233 (tp) cc_final: 0.8948 (mt) outliers start: 7 outliers final: 1 residues processed: 977 average time/residue: 0.4878 time to fit residues: 783.8915 Evaluate side-chains 678 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 676 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 404 optimal weight: 0.9980 chunk 275 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 362 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 248 optimal weight: 0.8980 chunk 436 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 228 HIS g 243 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 141 HIS d 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 39778 Z= 0.247 Angle : 0.674 18.157 53943 Z= 0.338 Chirality : 0.044 0.357 6456 Planarity : 0.005 0.061 6961 Dihedral : 6.256 102.020 5682 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 5149 helix: 0.57 (0.10), residues: 2840 sheet: -0.54 (0.20), residues: 603 loop : -0.59 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 15 HIS 0.007 0.001 HIS e 37 PHE 0.032 0.002 PHE b 95 TYR 0.025 0.002 TYR a 74 ARG 0.007 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 916 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.0969 (tt) cc_final: 0.0511 (mt) REVERT: a 84 LYS cc_start: 0.7794 (tttt) cc_final: 0.7569 (mtpp) REVERT: a 186 LEU cc_start: 0.7595 (mt) cc_final: 0.7092 (mt) REVERT: C 48 VAL cc_start: 0.9067 (t) cc_final: 0.8535 (t) REVERT: C 49 MET cc_start: 0.7772 (ptm) cc_final: 0.7192 (ptm) REVERT: C 184 ILE cc_start: 0.9307 (mt) cc_final: 0.9041 (mm) REVERT: C 194 CYS cc_start: 0.9042 (m) cc_final: 0.8662 (m) REVERT: C 258 LEU cc_start: 0.9422 (tp) cc_final: 0.9079 (tp) REVERT: C 274 MET cc_start: 0.8616 (mtm) cc_final: 0.8383 (mtt) REVERT: C 290 ASP cc_start: 0.8313 (m-30) cc_final: 0.7922 (t0) REVERT: C 409 ASN cc_start: 0.7937 (m-40) cc_final: 0.7644 (m-40) REVERT: C 480 LYS cc_start: 0.8818 (mttt) cc_final: 0.8435 (ptmt) REVERT: C 498 MET cc_start: 0.7976 (ttm) cc_final: 0.7018 (tpt) REVERT: D 90 GLU cc_start: 0.7833 (pm20) cc_final: 0.7455 (pm20) REVERT: D 183 MET cc_start: 0.9254 (mmm) cc_final: 0.8299 (mtt) REVERT: D 219 SER cc_start: 0.8349 (p) cc_final: 0.7630 (p) REVERT: D 247 MET cc_start: 0.8236 (mtp) cc_final: 0.7893 (mtm) REVERT: D 280 GLN cc_start: 0.8766 (pp30) cc_final: 0.8217 (pp30) REVERT: D 351 VAL cc_start: 0.9088 (t) cc_final: 0.8831 (p) REVERT: D 428 GLU cc_start: 0.8596 (pt0) cc_final: 0.8246 (pt0) REVERT: D 475 TYR cc_start: 0.7778 (t80) cc_final: 0.7026 (t80) REVERT: D 476 LEU cc_start: 0.9399 (mt) cc_final: 0.9132 (mt) REVERT: D 481 ASP cc_start: 0.8933 (m-30) cc_final: 0.8450 (p0) REVERT: E 66 ASN cc_start: 0.8994 (m-40) cc_final: 0.8482 (t0) REVERT: E 157 MET cc_start: 0.7455 (mpp) cc_final: 0.7202 (mpp) REVERT: E 191 ASN cc_start: 0.8399 (m-40) cc_final: 0.8048 (p0) REVERT: E 258 LEU cc_start: 0.9462 (tp) cc_final: 0.9219 (tp) REVERT: E 340 ASP cc_start: 0.8441 (m-30) cc_final: 0.7984 (m-30) REVERT: E 342 GLN cc_start: 0.8664 (pm20) cc_final: 0.7715 (pp30) REVERT: E 376 MET cc_start: 0.7748 (mmt) cc_final: 0.6452 (mmt) REVERT: E 436 MET cc_start: 0.7401 (ppp) cc_final: 0.7057 (ppp) REVERT: E 452 ASP cc_start: 0.8264 (m-30) cc_final: 0.7872 (t70) REVERT: E 497 GLN cc_start: 0.6350 (tp40) cc_final: 0.6046 (tp40) REVERT: F 26 ILE cc_start: 0.9441 (mt) cc_final: 0.9163 (mm) REVERT: F 59 MET cc_start: 0.6294 (tpp) cc_final: 0.5865 (tmm) REVERT: F 112 ASN cc_start: 0.8627 (m110) cc_final: 0.7921 (m110) REVERT: F 116 GLU cc_start: 0.8637 (pm20) cc_final: 0.7873 (pm20) REVERT: F 158 LEU cc_start: 0.9708 (tp) cc_final: 0.9470 (tp) REVERT: F 183 MET cc_start: 0.8554 (mmm) cc_final: 0.8341 (mmp) REVERT: F 184 GLU cc_start: 0.8485 (tp30) cc_final: 0.8262 (tt0) REVERT: F 241 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7930 (mm-30) REVERT: F 292 MET cc_start: 0.8998 (mtt) cc_final: 0.8662 (mtt) REVERT: F 314 THR cc_start: 0.8760 (p) cc_final: 0.8533 (p) REVERT: F 477 VAL cc_start: 0.9286 (m) cc_final: 0.8963 (p) REVERT: A 140 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8163 (mtt-85) REVERT: A 157 MET cc_start: 0.8834 (mpp) cc_final: 0.8103 (mpp) REVERT: A 267 GLN cc_start: 0.9256 (tt0) cc_final: 0.9041 (tt0) REVERT: A 296 SER cc_start: 0.9456 (p) cc_final: 0.9156 (t) REVERT: A 382 LYS cc_start: 0.8694 (mttt) cc_final: 0.7946 (pttm) REVERT: A 436 MET cc_start: 0.7754 (ppp) cc_final: 0.6998 (tmm) REVERT: B 79 MET cc_start: 0.8818 (mmm) cc_final: 0.8348 (mmm) REVERT: B 80 SER cc_start: 0.9448 (m) cc_final: 0.9191 (p) REVERT: B 167 LYS cc_start: 0.9118 (mppt) cc_final: 0.8641 (mppt) REVERT: B 213 TYR cc_start: 0.8101 (t80) cc_final: 0.7800 (t80) REVERT: B 298 TYR cc_start: 0.8357 (m-80) cc_final: 0.8117 (m-80) REVERT: B 370 SER cc_start: 0.9654 (m) cc_final: 0.9274 (p) REVERT: B 393 GLU cc_start: 0.8575 (pt0) cc_final: 0.8259 (pt0) REVERT: B 405 ILE cc_start: 0.9241 (pt) cc_final: 0.8983 (mt) REVERT: B 435 PHE cc_start: 0.8680 (m-80) cc_final: 0.7864 (m-80) REVERT: B 475 TYR cc_start: 0.8938 (t80) cc_final: 0.8523 (t80) REVERT: B 476 LEU cc_start: 0.8705 (mt) cc_final: 0.8286 (mt) REVERT: B 492 MET cc_start: 0.8308 (mtm) cc_final: 0.7844 (ptp) REVERT: e 94 GLN cc_start: 0.9086 (tt0) cc_final: 0.8649 (mt0) REVERT: e 111 GLN cc_start: 0.8877 (tt0) cc_final: 0.8322 (mp10) REVERT: e 112 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7540 (pttp) REVERT: g 98 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7021 (mm-30) REVERT: g 135 ASN cc_start: 0.8725 (m-40) cc_final: 0.8272 (t0) REVERT: g 136 MET cc_start: 0.8318 (tpp) cc_final: 0.7789 (tpp) REVERT: g 173 GLU cc_start: 0.7859 (pp20) cc_final: 0.7453 (tm-30) REVERT: g 282 LEU cc_start: 0.7380 (tp) cc_final: 0.7142 (pp) REVERT: g 284 PHE cc_start: 0.7400 (m-80) cc_final: 0.6261 (p90) REVERT: g 315 GLU cc_start: 0.8802 (tt0) cc_final: 0.8298 (tm-30) REVERT: S 60 MET cc_start: 0.5823 (mtm) cc_final: 0.4731 (mpp) REVERT: S 63 LEU cc_start: 0.6122 (mt) cc_final: 0.5799 (mt) REVERT: O 34 GLN cc_start: 0.7681 (mp10) cc_final: 0.7187 (mm110) REVERT: P 26 VAL cc_start: 0.6284 (m) cc_final: 0.6050 (p) REVERT: Q 60 MET cc_start: 0.1562 (ptm) cc_final: 0.1302 (ptp) REVERT: R 22 ILE cc_start: 0.6315 (mm) cc_final: 0.5970 (mm) REVERT: T 60 MET cc_start: 0.5270 (mmm) cc_final: 0.5010 (mmm) REVERT: G 60 MET cc_start: 0.4781 (ttt) cc_final: 0.4041 (ttt) REVERT: K 60 MET cc_start: 0.5100 (tpt) cc_final: 0.4750 (ttp) REVERT: I 59 PHE cc_start: 0.6853 (m-80) cc_final: 0.6565 (m-80) REVERT: p 102 PHE cc_start: 0.2778 (m-80) cc_final: 0.2380 (m-80) REVERT: p 152 ARG cc_start: 0.6116 (tpt170) cc_final: 0.5595 (mmp-170) REVERT: d 72 ASP cc_start: 0.7726 (t0) cc_final: 0.7370 (t0) REVERT: d 242 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8647 (pt0) outliers start: 3 outliers final: 1 residues processed: 917 average time/residue: 0.5072 time to fit residues: 775.9901 Evaluate side-chains 655 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 654 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 163 optimal weight: 5.9990 chunk 437 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 285 optimal weight: 0.0570 chunk 120 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 chunk 403 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 255 optimal weight: 0.0770 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 210 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 GLN H 34 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 39778 Z= 0.241 Angle : 0.664 15.587 53943 Z= 0.334 Chirality : 0.044 0.412 6456 Planarity : 0.005 0.062 6961 Dihedral : 6.121 98.077 5682 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 0.02 % Allowed : 2.61 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5149 helix: 0.65 (0.10), residues: 2799 sheet: -0.58 (0.20), residues: 620 loop : -0.57 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 15 HIS 0.006 0.001 HIS e 37 PHE 0.034 0.002 PHE b 95 TYR 0.023 0.002 TYR g 94 ARG 0.008 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 874 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.1029 (tt) cc_final: 0.0615 (mt) REVERT: a 84 LYS cc_start: 0.7816 (tttt) cc_final: 0.7582 (mtpp) REVERT: a 174 ILE cc_start: 0.7983 (pt) cc_final: 0.7715 (tp) REVERT: a 222 PHE cc_start: 0.8291 (t80) cc_final: 0.7783 (t80) REVERT: C 157 MET cc_start: 0.7946 (mmm) cc_final: 0.7730 (mmm) REVERT: C 184 ILE cc_start: 0.9298 (mt) cc_final: 0.9075 (mm) REVERT: C 194 CYS cc_start: 0.9069 (m) cc_final: 0.8603 (m) REVERT: C 223 ILE cc_start: 0.9256 (mp) cc_final: 0.8721 (tt) REVERT: C 258 LEU cc_start: 0.9403 (tp) cc_final: 0.9148 (tp) REVERT: C 290 ASP cc_start: 0.8285 (m-30) cc_final: 0.7899 (t0) REVERT: C 409 ASN cc_start: 0.7882 (m-40) cc_final: 0.7597 (m-40) REVERT: C 480 LYS cc_start: 0.8844 (mttt) cc_final: 0.8451 (ptmt) REVERT: C 498 MET cc_start: 0.8004 (ttm) cc_final: 0.7006 (tpt) REVERT: D 90 GLU cc_start: 0.7760 (pm20) cc_final: 0.7360 (pm20) REVERT: D 183 MET cc_start: 0.9305 (mmm) cc_final: 0.8327 (mtt) REVERT: D 219 SER cc_start: 0.8313 (p) cc_final: 0.7616 (p) REVERT: D 246 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.7839 (mtm-85) REVERT: D 280 GLN cc_start: 0.8795 (pp30) cc_final: 0.8155 (pp30) REVERT: D 351 VAL cc_start: 0.9079 (t) cc_final: 0.8798 (p) REVERT: D 428 GLU cc_start: 0.8680 (pt0) cc_final: 0.8259 (pt0) REVERT: D 475 TYR cc_start: 0.7817 (t80) cc_final: 0.7041 (t80) REVERT: D 476 LEU cc_start: 0.9399 (mt) cc_final: 0.9134 (mt) REVERT: D 481 ASP cc_start: 0.8943 (m-30) cc_final: 0.8469 (p0) REVERT: D 492 MET cc_start: 0.8244 (tmm) cc_final: 0.8029 (tmm) REVERT: E 66 ASN cc_start: 0.8990 (m-40) cc_final: 0.8619 (t0) REVERT: E 191 ASN cc_start: 0.8423 (m-40) cc_final: 0.8128 (p0) REVERT: E 241 TYR cc_start: 0.9259 (m-80) cc_final: 0.8956 (m-10) REVERT: E 251 MET cc_start: 0.8487 (ttt) cc_final: 0.7302 (tpp) REVERT: E 258 LEU cc_start: 0.9471 (tp) cc_final: 0.9185 (tp) REVERT: E 340 ASP cc_start: 0.8303 (m-30) cc_final: 0.7965 (m-30) REVERT: E 342 GLN cc_start: 0.8656 (pm20) cc_final: 0.7694 (pp30) REVERT: E 366 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7897 (mtm180) REVERT: E 376 MET cc_start: 0.7365 (mmt) cc_final: 0.6726 (mmt) REVERT: E 436 MET cc_start: 0.7496 (ppp) cc_final: 0.7179 (ppp) REVERT: E 452 ASP cc_start: 0.8266 (m-30) cc_final: 0.7913 (t70) REVERT: E 497 GLN cc_start: 0.6251 (tp40) cc_final: 0.5931 (tp40) REVERT: F 59 MET cc_start: 0.6270 (tpp) cc_final: 0.5977 (tmm) REVERT: F 112 ASN cc_start: 0.8634 (m110) cc_final: 0.7911 (m110) REVERT: F 116 GLU cc_start: 0.8596 (pm20) cc_final: 0.7820 (pm20) REVERT: F 158 LEU cc_start: 0.9696 (tp) cc_final: 0.9491 (tp) REVERT: F 184 GLU cc_start: 0.8500 (tp30) cc_final: 0.8167 (tp30) REVERT: F 212 LEU cc_start: 0.8732 (tp) cc_final: 0.7617 (tp) REVERT: F 216 MET cc_start: 0.8376 (mpp) cc_final: 0.7896 (mpp) REVERT: F 241 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7868 (mm-30) REVERT: F 254 LEU cc_start: 0.9296 (tp) cc_final: 0.8885 (tp) REVERT: F 292 MET cc_start: 0.9039 (mtt) cc_final: 0.8700 (mtt) REVERT: F 314 THR cc_start: 0.8785 (p) cc_final: 0.8552 (p) REVERT: F 477 VAL cc_start: 0.9292 (m) cc_final: 0.8974 (p) REVERT: A 67 LEU cc_start: 0.9353 (mt) cc_final: 0.9101 (mt) REVERT: A 140 ARG cc_start: 0.8755 (mtt180) cc_final: 0.8117 (mtt-85) REVERT: A 157 MET cc_start: 0.8819 (mpp) cc_final: 0.8162 (mpp) REVERT: A 219 MET cc_start: 0.8503 (tpp) cc_final: 0.8259 (tpp) REVERT: A 267 GLN cc_start: 0.9310 (tt0) cc_final: 0.9048 (tt0) REVERT: A 296 SER cc_start: 0.9518 (p) cc_final: 0.9127 (t) REVERT: A 309 LEU cc_start: 0.8941 (mt) cc_final: 0.8511 (tt) REVERT: A 383 LEU cc_start: 0.8699 (tp) cc_final: 0.8488 (tp) REVERT: A 436 MET cc_start: 0.7716 (ppp) cc_final: 0.7070 (tmm) REVERT: B 79 MET cc_start: 0.8864 (mmm) cc_final: 0.8355 (mmm) REVERT: B 80 SER cc_start: 0.9464 (m) cc_final: 0.9201 (p) REVERT: B 168 ILE cc_start: 0.9563 (mm) cc_final: 0.9170 (mm) REVERT: B 213 TYR cc_start: 0.8110 (t80) cc_final: 0.7765 (t80) REVERT: B 241 GLU cc_start: 0.8715 (mp0) cc_final: 0.8390 (mp0) REVERT: B 298 TYR cc_start: 0.8357 (m-80) cc_final: 0.8022 (m-80) REVERT: B 370 SER cc_start: 0.9655 (m) cc_final: 0.9273 (p) REVERT: B 435 PHE cc_start: 0.8571 (m-80) cc_final: 0.7825 (m-80) REVERT: B 475 TYR cc_start: 0.9036 (t80) cc_final: 0.8599 (t80) REVERT: B 476 LEU cc_start: 0.8775 (mt) cc_final: 0.8118 (mt) REVERT: B 492 MET cc_start: 0.8363 (mtm) cc_final: 0.8162 (ptp) REVERT: e 3 LEU cc_start: 0.7208 (pp) cc_final: 0.6628 (mp) REVERT: e 40 THR cc_start: 0.4888 (m) cc_final: 0.4595 (m) REVERT: e 94 GLN cc_start: 0.9072 (tt0) cc_final: 0.8638 (mt0) REVERT: e 111 GLN cc_start: 0.8858 (tt0) cc_final: 0.8314 (mp10) REVERT: e 112 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7551 (pttp) REVERT: g 135 ASN cc_start: 0.8764 (m-40) cc_final: 0.8333 (t0) REVERT: g 136 MET cc_start: 0.8343 (tpp) cc_final: 0.7822 (tpp) REVERT: g 163 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7071 (tppt) REVERT: g 173 GLU cc_start: 0.7831 (pp20) cc_final: 0.7473 (pp20) REVERT: g 282 LEU cc_start: 0.7345 (tp) cc_final: 0.7132 (pp) REVERT: g 284 PHE cc_start: 0.7394 (m-80) cc_final: 0.6274 (p90) REVERT: g 315 GLU cc_start: 0.8494 (tt0) cc_final: 0.8047 (tm-30) REVERT: g 316 LEU cc_start: 0.8880 (mt) cc_final: 0.8623 (mt) REVERT: S 36 VAL cc_start: 0.6539 (t) cc_final: 0.6291 (t) REVERT: S 60 MET cc_start: 0.5511 (mtm) cc_final: 0.5158 (mmm) REVERT: S 63 LEU cc_start: 0.6183 (mt) cc_final: 0.5790 (mt) REVERT: O 34 GLN cc_start: 0.7642 (mp10) cc_final: 0.7342 (mm110) REVERT: Q 60 MET cc_start: 0.1429 (ptm) cc_final: 0.1201 (ptp) REVERT: G 60 MET cc_start: 0.4717 (ttt) cc_final: 0.3999 (ttt) REVERT: J 28 GLN cc_start: 0.6154 (mt0) cc_final: 0.5370 (tt0) REVERT: J 46 GLU cc_start: 0.3453 (tt0) cc_final: 0.3251 (tt0) REVERT: I 39 ILE cc_start: 0.7194 (tt) cc_final: 0.6931 (pt) REVERT: p 102 PHE cc_start: 0.2791 (m-80) cc_final: 0.2455 (m-80) REVERT: p 139 GLN cc_start: 0.3647 (mm-40) cc_final: 0.3001 (mm110) REVERT: p 152 ARG cc_start: 0.6141 (tpt170) cc_final: 0.5681 (mmp-170) REVERT: b 179 MET cc_start: 0.5649 (ppp) cc_final: 0.5381 (ppp) REVERT: d 242 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8618 (pt0) outliers start: 1 outliers final: 0 residues processed: 874 average time/residue: 0.5031 time to fit residues: 735.1295 Evaluate side-chains 664 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 469 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 277 optimal weight: 9.9990 chunk 355 optimal weight: 0.9990 chunk 275 optimal weight: 0.2980 chunk 409 optimal weight: 20.0000 chunk 271 optimal weight: 0.6980 chunk 484 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 295 optimal weight: 0.3980 chunk 223 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS a 34 GLN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN E 214 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN B 210 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 243 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 GLN K 42 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39778 Z= 0.190 Angle : 0.646 11.339 53943 Z= 0.322 Chirality : 0.043 0.316 6456 Planarity : 0.005 0.061 6961 Dihedral : 5.842 87.888 5682 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 0.07 % Allowed : 1.75 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.12), residues: 5149 helix: 0.71 (0.10), residues: 2789 sheet: -0.37 (0.20), residues: 612 loop : -0.57 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 117 HIS 0.004 0.001 HIS D 133 PHE 0.032 0.002 PHE b 95 TYR 0.023 0.001 TYR B 259 ARG 0.011 0.001 ARG b 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 913 time to evaluate : 4.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 56 ILE cc_start: 0.0956 (tt) cc_final: 0.0723 (mt) REVERT: a 174 ILE cc_start: 0.7966 (pt) cc_final: 0.7716 (tp) REVERT: a 222 PHE cc_start: 0.8237 (t80) cc_final: 0.7760 (t80) REVERT: C 82 MET cc_start: 0.8013 (tpp) cc_final: 0.7713 (tpp) REVERT: C 194 CYS cc_start: 0.8956 (m) cc_final: 0.8691 (m) REVERT: C 223 ILE cc_start: 0.9250 (mp) cc_final: 0.9048 (mt) REVERT: C 290 ASP cc_start: 0.8084 (m-30) cc_final: 0.7783 (t0) REVERT: C 405 LYS cc_start: 0.8066 (tptp) cc_final: 0.7349 (tptp) REVERT: C 409 ASN cc_start: 0.7948 (m-40) cc_final: 0.7419 (m-40) REVERT: C 451 LEU cc_start: 0.8335 (tt) cc_final: 0.7900 (tt) REVERT: C 480 LYS cc_start: 0.8796 (mttt) cc_final: 0.8419 (ptmt) REVERT: C 487 GLU cc_start: 0.8099 (pp20) cc_final: 0.7882 (pp20) REVERT: C 498 MET cc_start: 0.7762 (ttm) cc_final: 0.6841 (tpt) REVERT: D 90 GLU cc_start: 0.7777 (pm20) cc_final: 0.7337 (pm20) REVERT: D 183 MET cc_start: 0.9209 (mmm) cc_final: 0.8306 (mtt) REVERT: D 219 SER cc_start: 0.8379 (p) cc_final: 0.7503 (p) REVERT: D 246 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: D 280 GLN cc_start: 0.8700 (pp30) cc_final: 0.7996 (pp30) REVERT: D 351 VAL cc_start: 0.9046 (t) cc_final: 0.8784 (p) REVERT: D 428 GLU cc_start: 0.8643 (pt0) cc_final: 0.8252 (pt0) REVERT: D 475 TYR cc_start: 0.7723 (t80) cc_final: 0.6990 (t80) REVERT: D 476 LEU cc_start: 0.9368 (mt) cc_final: 0.9123 (mt) REVERT: D 481 ASP cc_start: 0.8903 (m-30) cc_final: 0.8437 (p0) REVERT: D 492 MET cc_start: 0.8249 (tmm) cc_final: 0.8022 (tmm) REVERT: E 66 ASN cc_start: 0.8960 (m-40) cc_final: 0.8582 (t0) REVERT: E 74 VAL cc_start: 0.9110 (t) cc_final: 0.8862 (p) REVERT: E 251 MET cc_start: 0.8389 (ttt) cc_final: 0.7267 (tpp) REVERT: E 258 LEU cc_start: 0.9421 (tp) cc_final: 0.9219 (tp) REVERT: E 342 GLN cc_start: 0.8618 (pm20) cc_final: 0.7706 (pp30) REVERT: E 376 MET cc_start: 0.7362 (mmt) cc_final: 0.6774 (mmt) REVERT: E 436 MET cc_start: 0.7465 (ppp) cc_final: 0.7134 (ppp) REVERT: E 452 ASP cc_start: 0.8363 (m-30) cc_final: 0.7966 (t70) REVERT: E 497 GLN cc_start: 0.6059 (tp40) cc_final: 0.5780 (tp40) REVERT: F 39 LYS cc_start: 0.8615 (mppt) cc_final: 0.8200 (mttm) REVERT: F 59 MET cc_start: 0.6142 (tpp) cc_final: 0.5930 (tmm) REVERT: F 112 ASN cc_start: 0.8633 (m110) cc_final: 0.7748 (m-40) REVERT: F 116 GLU cc_start: 0.8610 (pm20) cc_final: 0.7801 (pm20) REVERT: F 184 GLU cc_start: 0.8477 (tp30) cc_final: 0.8207 (tp30) REVERT: F 241 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7877 (mm-30) REVERT: F 254 LEU cc_start: 0.9194 (tp) cc_final: 0.8791 (tp) REVERT: F 292 MET cc_start: 0.9048 (mtt) cc_final: 0.8736 (mtt) REVERT: F 477 VAL cc_start: 0.9249 (m) cc_final: 0.8930 (p) REVERT: A 37 ASP cc_start: 0.7479 (t0) cc_final: 0.7276 (t0) REVERT: A 67 LEU cc_start: 0.9237 (mt) cc_final: 0.8989 (mt) REVERT: A 140 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8057 (mtt-85) REVERT: A 157 MET cc_start: 0.8668 (mpp) cc_final: 0.8056 (mpp) REVERT: A 219 MET cc_start: 0.8368 (tpp) cc_final: 0.8168 (tpp) REVERT: A 267 GLN cc_start: 0.9222 (tt0) cc_final: 0.8612 (tm-30) REVERT: A 296 SER cc_start: 0.9448 (p) cc_final: 0.8943 (t) REVERT: A 309 LEU cc_start: 0.8852 (mt) cc_final: 0.8540 (tt) REVERT: A 382 LYS cc_start: 0.8492 (mttt) cc_final: 0.8082 (mmmm) REVERT: A 436 MET cc_start: 0.7698 (ppp) cc_final: 0.7038 (ppp) REVERT: B 79 MET cc_start: 0.8770 (mmm) cc_final: 0.8238 (mmp) REVERT: B 80 SER cc_start: 0.9486 (m) cc_final: 0.9233 (p) REVERT: B 168 ILE cc_start: 0.9569 (mm) cc_final: 0.9146 (mm) REVERT: B 213 TYR cc_start: 0.8043 (t80) cc_final: 0.7735 (t80) REVERT: B 298 TYR cc_start: 0.8107 (m-80) cc_final: 0.7838 (m-80) REVERT: B 299 GLN cc_start: 0.8710 (pm20) cc_final: 0.8361 (pt0) REVERT: B 370 SER cc_start: 0.9635 (m) cc_final: 0.9296 (p) REVERT: B 408 LEU cc_start: 0.9080 (mt) cc_final: 0.8837 (mp) REVERT: B 411 ASP cc_start: 0.7144 (t70) cc_final: 0.6892 (t0) REVERT: B 435 PHE cc_start: 0.8440 (m-80) cc_final: 0.7640 (m-80) REVERT: B 475 TYR cc_start: 0.8975 (t80) cc_final: 0.8427 (t80) REVERT: B 476 LEU cc_start: 0.8699 (mt) cc_final: 0.7990 (mt) REVERT: e 3 LEU cc_start: 0.6823 (pp) cc_final: 0.6509 (mp) REVERT: e 94 GLN cc_start: 0.9069 (tt0) cc_final: 0.8696 (mt0) REVERT: e 111 GLN cc_start: 0.8856 (tt0) cc_final: 0.8305 (mp10) REVERT: e 112 LYS cc_start: 0.8014 (mmtm) cc_final: 0.7528 (pttp) REVERT: g 135 ASN cc_start: 0.8709 (m-40) cc_final: 0.8209 (t0) REVERT: g 136 MET cc_start: 0.8142 (tpp) cc_final: 0.7520 (tpp) REVERT: g 163 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7027 (tppt) REVERT: g 173 GLU cc_start: 0.7798 (pp20) cc_final: 0.7406 (tm-30) REVERT: g 192 GLN cc_start: 0.8248 (tp40) cc_final: 0.6980 (tp40) REVERT: g 196 ASP cc_start: 0.8507 (m-30) cc_final: 0.8072 (m-30) REVERT: g 282 LEU cc_start: 0.7315 (tp) cc_final: 0.7064 (pp) REVERT: g 284 PHE cc_start: 0.7355 (m-80) cc_final: 0.6226 (p90) REVERT: g 315 GLU cc_start: 0.8503 (tt0) cc_final: 0.8097 (tm-30) REVERT: g 316 LEU cc_start: 0.8848 (mt) cc_final: 0.8534 (mt) REVERT: S 36 VAL cc_start: 0.6496 (t) cc_final: 0.6224 (t) REVERT: S 63 LEU cc_start: 0.5793 (mt) cc_final: 0.5482 (mt) REVERT: P 75 LEU cc_start: 0.7203 (mt) cc_final: 0.6406 (mm) REVERT: T 60 MET cc_start: 0.5349 (mmm) cc_final: 0.4821 (mmm) REVERT: G 60 MET cc_start: 0.4815 (ttt) cc_final: 0.4044 (ttt) REVERT: K 60 MET cc_start: 0.5285 (tpt) cc_final: 0.4771 (ttp) REVERT: K 68 LEU cc_start: 0.6340 (tt) cc_final: 0.5942 (tt) REVERT: J 28 GLN cc_start: 0.6198 (mt0) cc_final: 0.5161 (tt0) REVERT: p 102 PHE cc_start: 0.2851 (m-80) cc_final: 0.2368 (m-80) REVERT: p 152 ARG cc_start: 0.6211 (tpt170) cc_final: 0.5813 (mmp-170) REVERT: d 186 LEU cc_start: 0.5529 (pp) cc_final: 0.5160 (mt) REVERT: d 188 ASN cc_start: 0.7577 (m110) cc_final: 0.7308 (m110) outliers start: 3 outliers final: 0 residues processed: 914 average time/residue: 0.4739 time to fit residues: 718.3731 Evaluate side-chains 687 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 299 optimal weight: 0.3980 chunk 193 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 381 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN B 210 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 143 GLN b 23 ASN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 146 GLN d 147 ASN d 190 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 39778 Z= 0.199 Angle : 0.661 10.468 53943 Z= 0.331 Chirality : 0.043 0.282 6456 Planarity : 0.005 0.071 6961 Dihedral : 5.653 75.687 5682 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 0.05 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.12), residues: 5149 helix: 0.70 (0.10), residues: 2782 sheet: -0.39 (0.20), residues: 607 loop : -0.58 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 117 HIS 0.005 0.001 HIS e 37 PHE 0.033 0.002 PHE a 97 TYR 0.036 0.001 TYR L 66 ARG 0.012 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 918 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 117 TRP cc_start: 0.4193 (m-10) cc_final: 0.3959 (m-10) REVERT: a 174 ILE cc_start: 0.7967 (pt) cc_final: 0.7739 (tp) REVERT: a 222 PHE cc_start: 0.8174 (t80) cc_final: 0.7336 (t80) REVERT: C 77 MET cc_start: 0.8518 (mtp) cc_final: 0.8250 (mtp) REVERT: C 82 MET cc_start: 0.8050 (tpp) cc_final: 0.7712 (tpp) REVERT: C 219 MET cc_start: 0.8840 (mmp) cc_final: 0.8334 (mmp) REVERT: C 223 ILE cc_start: 0.9241 (mp) cc_final: 0.8964 (mt) REVERT: C 290 ASP cc_start: 0.8071 (m-30) cc_final: 0.7712 (t0) REVERT: C 405 LYS cc_start: 0.8150 (tptp) cc_final: 0.7327 (tptp) REVERT: C 409 ASN cc_start: 0.8038 (m-40) cc_final: 0.7374 (m-40) REVERT: C 480 LYS cc_start: 0.8702 (mttt) cc_final: 0.8368 (ptmt) REVERT: C 487 GLU cc_start: 0.8068 (pp20) cc_final: 0.7854 (pp20) REVERT: C 498 MET cc_start: 0.7841 (ttm) cc_final: 0.6928 (tpt) REVERT: D 183 MET cc_start: 0.9202 (mmm) cc_final: 0.8091 (mtt) REVERT: D 219 SER cc_start: 0.8421 (p) cc_final: 0.7550 (p) REVERT: D 246 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: D 247 MET cc_start: 0.8113 (mmm) cc_final: 0.7882 (mmm) REVERT: D 280 GLN cc_start: 0.8903 (pp30) cc_final: 0.8096 (pp30) REVERT: D 336 ASP cc_start: 0.9311 (t0) cc_final: 0.9046 (t0) REVERT: D 351 VAL cc_start: 0.9023 (t) cc_final: 0.8767 (p) REVERT: D 428 GLU cc_start: 0.8672 (pt0) cc_final: 0.8287 (pt0) REVERT: D 475 TYR cc_start: 0.7703 (t80) cc_final: 0.6921 (t80) REVERT: D 476 LEU cc_start: 0.9352 (mt) cc_final: 0.9147 (mt) REVERT: D 481 ASP cc_start: 0.8886 (m-30) cc_final: 0.8367 (p0) REVERT: E 55 GLU cc_start: 0.8348 (tp30) cc_final: 0.8105 (tp30) REVERT: E 66 ASN cc_start: 0.8943 (m-40) cc_final: 0.8546 (t0) REVERT: E 74 VAL cc_start: 0.9125 (t) cc_final: 0.8864 (p) REVERT: E 157 MET cc_start: 0.7793 (mpp) cc_final: 0.7421 (mpp) REVERT: E 241 TYR cc_start: 0.9136 (m-80) cc_final: 0.8836 (m-80) REVERT: E 251 MET cc_start: 0.8441 (ttt) cc_final: 0.7343 (tpp) REVERT: E 258 LEU cc_start: 0.9396 (tp) cc_final: 0.9179 (tp) REVERT: E 340 ASP cc_start: 0.8194 (m-30) cc_final: 0.7863 (m-30) REVERT: E 342 GLN cc_start: 0.8580 (pm20) cc_final: 0.7692 (pp30) REVERT: E 376 MET cc_start: 0.7404 (mmt) cc_final: 0.6780 (mmt) REVERT: E 409 ASN cc_start: 0.8620 (m-40) cc_final: 0.8267 (t0) REVERT: E 436 MET cc_start: 0.7427 (ppp) cc_final: 0.7023 (ppp) REVERT: E 497 GLN cc_start: 0.6058 (tp40) cc_final: 0.5695 (tp40) REVERT: E 498 MET cc_start: 0.7091 (tpp) cc_final: 0.6841 (mmm) REVERT: F 39 LYS cc_start: 0.8704 (mppt) cc_final: 0.8387 (mttm) REVERT: F 59 MET cc_start: 0.6186 (tpp) cc_final: 0.5854 (tmm) REVERT: F 112 ASN cc_start: 0.8732 (m110) cc_final: 0.7896 (m-40) REVERT: F 116 GLU cc_start: 0.8603 (pm20) cc_final: 0.7834 (pm20) REVERT: F 158 LEU cc_start: 0.9683 (tp) cc_final: 0.9418 (tp) REVERT: F 184 GLU cc_start: 0.8386 (tp30) cc_final: 0.8124 (tp30) REVERT: F 254 LEU cc_start: 0.9102 (tp) cc_final: 0.8724 (tp) REVERT: F 292 MET cc_start: 0.9043 (mtt) cc_final: 0.8708 (mtt) REVERT: F 477 VAL cc_start: 0.9239 (m) cc_final: 0.8931 (p) REVERT: A 37 ASP cc_start: 0.7334 (t0) cc_final: 0.7100 (t0) REVERT: A 52 GLU cc_start: 0.8795 (tt0) cc_final: 0.8405 (tt0) REVERT: A 67 LEU cc_start: 0.9198 (mt) cc_final: 0.8930 (mt) REVERT: A 140 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8038 (mtt-85) REVERT: A 157 MET cc_start: 0.8644 (mpp) cc_final: 0.8134 (mpp) REVERT: A 219 MET cc_start: 0.8490 (tpp) cc_final: 0.8204 (tpp) REVERT: A 267 GLN cc_start: 0.9209 (tt0) cc_final: 0.8900 (tt0) REVERT: A 290 ASP cc_start: 0.7701 (p0) cc_final: 0.7416 (p0) REVERT: A 296 SER cc_start: 0.9363 (p) cc_final: 0.8820 (t) REVERT: A 309 LEU cc_start: 0.8856 (mt) cc_final: 0.8619 (tt) REVERT: A 382 LYS cc_start: 0.8452 (mttt) cc_final: 0.8058 (mmmm) REVERT: A 436 MET cc_start: 0.7636 (ppp) cc_final: 0.7307 (tmm) REVERT: A 499 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7677 (mm-30) REVERT: B 79 MET cc_start: 0.8636 (mmm) cc_final: 0.8072 (mmm) REVERT: B 80 SER cc_start: 0.9423 (m) cc_final: 0.9220 (p) REVERT: B 168 ILE cc_start: 0.9568 (mm) cc_final: 0.9113 (mm) REVERT: B 213 TYR cc_start: 0.8032 (t80) cc_final: 0.7684 (t80) REVERT: B 298 TYR cc_start: 0.8146 (m-80) cc_final: 0.7870 (m-80) REVERT: B 299 GLN cc_start: 0.8574 (pm20) cc_final: 0.8170 (pt0) REVERT: B 370 SER cc_start: 0.9656 (m) cc_final: 0.9265 (p) REVERT: B 411 ASP cc_start: 0.7177 (t70) cc_final: 0.6753 (t0) REVERT: B 435 PHE cc_start: 0.8415 (m-80) cc_final: 0.7603 (m-80) REVERT: B 462 LEU cc_start: 0.8735 (tp) cc_final: 0.8374 (tt) REVERT: B 475 TYR cc_start: 0.8922 (t80) cc_final: 0.8552 (t80) REVERT: B 476 LEU cc_start: 0.8510 (mt) cc_final: 0.8048 (mt) REVERT: e 3 LEU cc_start: 0.6753 (pp) cc_final: 0.6153 (mp) REVERT: e 94 GLN cc_start: 0.9024 (tt0) cc_final: 0.8655 (mt0) REVERT: e 111 GLN cc_start: 0.8808 (tt0) cc_final: 0.8256 (mp10) REVERT: e 112 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7607 (pttp) REVERT: g 135 ASN cc_start: 0.8683 (m-40) cc_final: 0.8188 (t0) REVERT: g 136 MET cc_start: 0.8127 (tpp) cc_final: 0.7515 (tpp) REVERT: g 144 ARG cc_start: 0.9051 (mmm160) cc_final: 0.8354 (mmm160) REVERT: g 163 LYS cc_start: 0.7294 (mmtt) cc_final: 0.7019 (tppt) REVERT: g 173 GLU cc_start: 0.7771 (pp20) cc_final: 0.7463 (tm-30) REVERT: g 192 GLN cc_start: 0.7865 (tp40) cc_final: 0.7007 (tp40) REVERT: g 196 ASP cc_start: 0.8393 (m-30) cc_final: 0.7980 (m-30) REVERT: g 284 PHE cc_start: 0.7294 (m-80) cc_final: 0.6225 (p90) REVERT: g 315 GLU cc_start: 0.8555 (tt0) cc_final: 0.8219 (tm-30) REVERT: S 36 VAL cc_start: 0.6488 (t) cc_final: 0.6235 (t) REVERT: S 63 LEU cc_start: 0.5474 (mt) cc_final: 0.5098 (mt) REVERT: S 75 LEU cc_start: 0.7376 (tp) cc_final: 0.6380 (mm) REVERT: P 60 MET cc_start: 0.7896 (ppp) cc_final: 0.7688 (ppp) REVERT: T 60 MET cc_start: 0.5445 (mmm) cc_final: 0.4934 (mmm) REVERT: G 36 VAL cc_start: 0.8019 (t) cc_final: 0.7523 (p) REVERT: G 60 MET cc_start: 0.4974 (ttt) cc_final: 0.4245 (ttt) REVERT: H 37 GLU cc_start: 0.6749 (pp20) cc_final: 0.6531 (pp20) REVERT: K 60 MET cc_start: 0.5310 (tpt) cc_final: 0.4794 (ttp) REVERT: J 28 GLN cc_start: 0.6171 (mt0) cc_final: 0.5069 (tt0) REVERT: p 102 PHE cc_start: 0.3040 (m-80) cc_final: 0.2538 (m-80) outliers start: 2 outliers final: 0 residues processed: 918 average time/residue: 0.4793 time to fit residues: 732.6415 Evaluate side-chains 686 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 441 optimal weight: 2.9990 chunk 464 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 408 optimal weight: 10.0000 chunk 427 optimal weight: 10.0000 chunk 450 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN D 310 GLN D 325 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN F 66 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 351 ASN A 410 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 30 GLN e 93 GLN g 97 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 206 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 39778 Z= 0.401 Angle : 0.775 10.473 53943 Z= 0.393 Chirality : 0.047 0.291 6456 Planarity : 0.006 0.074 6961 Dihedral : 6.021 74.466 5682 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 0.05 % Allowed : 0.93 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 5149 helix: 0.46 (0.10), residues: 2791 sheet: -0.69 (0.20), residues: 634 loop : -0.57 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP e 15 HIS 0.008 0.001 HIS C 43 PHE 0.047 0.003 PHE F 343 TYR 0.032 0.002 TYR a 74 ARG 0.010 0.001 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 811 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 117 TRP cc_start: 0.4430 (m-10) cc_final: 0.4128 (m-10) REVERT: a 174 ILE cc_start: 0.7977 (pt) cc_final: 0.7741 (tp) REVERT: C 77 MET cc_start: 0.8681 (mtp) cc_final: 0.8269 (mtp) REVERT: C 157 MET cc_start: 0.7988 (mmm) cc_final: 0.7655 (mmm) REVERT: C 184 ILE cc_start: 0.9025 (mm) cc_final: 0.8701 (mm) REVERT: C 219 MET cc_start: 0.8891 (mmp) cc_final: 0.8423 (mmp) REVERT: C 223 ILE cc_start: 0.9249 (mp) cc_final: 0.9000 (mt) REVERT: C 290 ASP cc_start: 0.8313 (m-30) cc_final: 0.7859 (t0) REVERT: C 409 ASN cc_start: 0.7987 (m-40) cc_final: 0.7703 (m-40) REVERT: C 417 LEU cc_start: 0.9296 (mt) cc_final: 0.8882 (mt) REVERT: C 480 LYS cc_start: 0.8820 (mttt) cc_final: 0.8517 (ptmt) REVERT: C 498 MET cc_start: 0.7864 (ttm) cc_final: 0.6832 (tpt) REVERT: D 183 MET cc_start: 0.9270 (mmm) cc_final: 0.8369 (mtt) REVERT: D 247 MET cc_start: 0.8377 (mmm) cc_final: 0.8087 (mmm) REVERT: D 280 GLN cc_start: 0.9058 (pp30) cc_final: 0.8573 (pp30) REVERT: D 336 ASP cc_start: 0.9473 (t0) cc_final: 0.9079 (t0) REVERT: D 428 GLU cc_start: 0.8725 (pt0) cc_final: 0.8444 (pt0) REVERT: D 475 TYR cc_start: 0.8061 (t80) cc_final: 0.7482 (t80) REVERT: D 481 ASP cc_start: 0.9001 (m-30) cc_final: 0.8511 (p0) REVERT: E 22 ARG cc_start: 0.6943 (mpp80) cc_final: 0.6718 (mpp80) REVERT: E 55 GLU cc_start: 0.8380 (tp30) cc_final: 0.8146 (tp30) REVERT: E 74 VAL cc_start: 0.9247 (t) cc_final: 0.9032 (p) REVERT: E 157 MET cc_start: 0.7730 (mpp) cc_final: 0.7109 (mpp) REVERT: E 251 MET cc_start: 0.8546 (ttt) cc_final: 0.7461 (tpp) REVERT: E 258 LEU cc_start: 0.9388 (tp) cc_final: 0.9019 (tp) REVERT: E 340 ASP cc_start: 0.8199 (m-30) cc_final: 0.7747 (m-30) REVERT: E 342 GLN cc_start: 0.8794 (pm20) cc_final: 0.7697 (pp30) REVERT: E 408 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8234 (tm-30) REVERT: E 436 MET cc_start: 0.7303 (ppp) cc_final: 0.6938 (ppp) REVERT: E 497 GLN cc_start: 0.6197 (tp40) cc_final: 0.5823 (tp40) REVERT: F 32 ASP cc_start: 0.5504 (m-30) cc_final: 0.5247 (m-30) REVERT: F 39 LYS cc_start: 0.8923 (mppt) cc_final: 0.8450 (mttt) REVERT: F 59 MET cc_start: 0.6406 (tpp) cc_final: 0.6117 (tmm) REVERT: F 79 MET cc_start: 0.9192 (mmt) cc_final: 0.8853 (mmt) REVERT: F 112 ASN cc_start: 0.8574 (m110) cc_final: 0.8166 (m110) REVERT: F 184 GLU cc_start: 0.8561 (tp30) cc_final: 0.8269 (tp30) REVERT: F 254 LEU cc_start: 0.9218 (tp) cc_final: 0.8751 (tp) REVERT: F 292 MET cc_start: 0.9190 (mtt) cc_final: 0.8867 (mtt) REVERT: F 419 LEU cc_start: 0.8555 (tt) cc_final: 0.8248 (mt) REVERT: F 477 VAL cc_start: 0.9355 (m) cc_final: 0.9090 (p) REVERT: F 488 MET cc_start: 0.8455 (ppp) cc_final: 0.7777 (mtt) REVERT: A 13 ILE cc_start: 0.8053 (tp) cc_final: 0.7759 (tp) REVERT: A 37 ASP cc_start: 0.7731 (t0) cc_final: 0.7479 (t0) REVERT: A 140 ARG cc_start: 0.8756 (mtt180) cc_final: 0.8138 (mtt-85) REVERT: A 157 MET cc_start: 0.8856 (mpp) cc_final: 0.8251 (mpp) REVERT: A 296 SER cc_start: 0.9453 (p) cc_final: 0.9121 (t) REVERT: A 382 LYS cc_start: 0.8594 (mttt) cc_final: 0.8286 (mmtp) REVERT: A 436 MET cc_start: 0.7974 (ppp) cc_final: 0.7337 (ppp) REVERT: A 458 LEU cc_start: 0.9038 (tp) cc_final: 0.8760 (tp) REVERT: B 79 MET cc_start: 0.8790 (mmm) cc_final: 0.8238 (mmm) REVERT: B 168 ILE cc_start: 0.9536 (mm) cc_final: 0.9200 (mm) REVERT: B 204 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6914 (mm-30) REVERT: B 274 ASN cc_start: 0.8785 (t0) cc_final: 0.8533 (t0) REVERT: B 370 SER cc_start: 0.9644 (m) cc_final: 0.9146 (p) REVERT: B 399 LYS cc_start: 0.9244 (ttpt) cc_final: 0.9002 (tppt) REVERT: B 411 ASP cc_start: 0.7213 (t70) cc_final: 0.6489 (t0) REVERT: B 435 PHE cc_start: 0.8703 (m-80) cc_final: 0.8022 (m-80) REVERT: B 475 TYR cc_start: 0.9117 (t80) cc_final: 0.8642 (t80) REVERT: B 476 LEU cc_start: 0.8742 (mt) cc_final: 0.8188 (mt) REVERT: e 55 ASP cc_start: 0.6019 (p0) cc_final: 0.5701 (t0) REVERT: e 111 GLN cc_start: 0.8849 (tt0) cc_final: 0.8349 (mp10) REVERT: e 112 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7647 (pttp) REVERT: g 135 ASN cc_start: 0.8872 (m-40) cc_final: 0.8446 (t0) REVERT: g 136 MET cc_start: 0.8524 (tpp) cc_final: 0.7930 (tpp) REVERT: g 144 ARG cc_start: 0.9133 (mmm160) cc_final: 0.8502 (mmm160) REVERT: g 163 LYS cc_start: 0.7637 (mmtt) cc_final: 0.7360 (tppt) REVERT: g 173 GLU cc_start: 0.7862 (pp20) cc_final: 0.7486 (pp20) REVERT: g 192 GLN cc_start: 0.8362 (tp40) cc_final: 0.7221 (tp40) REVERT: g 196 ASP cc_start: 0.8581 (m-30) cc_final: 0.8141 (m-30) REVERT: g 315 GLU cc_start: 0.8754 (tt0) cc_final: 0.8299 (tm-30) REVERT: g 320 MET cc_start: 0.8571 (tmm) cc_final: 0.8368 (tmm) REVERT: S 34 GLN cc_start: 0.6128 (tt0) cc_final: 0.5629 (tt0) REVERT: O 68 LEU cc_start: 0.6856 (tp) cc_final: 0.6284 (tp) REVERT: T 60 MET cc_start: 0.5468 (mmm) cc_final: 0.5211 (mmm) REVERT: G 34 GLN cc_start: 0.5634 (tt0) cc_final: 0.5400 (tt0) REVERT: G 60 MET cc_start: 0.4814 (ttt) cc_final: 0.4032 (ttt) REVERT: L 52 THR cc_start: 0.6416 (m) cc_final: 0.6200 (p) REVERT: J 28 GLN cc_start: 0.6671 (mt0) cc_final: 0.5693 (tt0) REVERT: J 53 LEU cc_start: 0.7115 (tp) cc_final: 0.6769 (tp) REVERT: I 50 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7062 (ttp-170) REVERT: p 102 PHE cc_start: 0.3282 (m-80) cc_final: 0.2803 (m-80) REVERT: b 179 MET cc_start: 0.5806 (ppp) cc_final: 0.5399 (ppp) outliers start: 2 outliers final: 0 residues processed: 811 average time/residue: 0.4870 time to fit residues: 657.6381 Evaluate side-chains 619 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 296 optimal weight: 1.9990 chunk 477 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 501 optimal weight: 6.9990 chunk 461 optimal weight: 7.9990 chunk 399 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 308 optimal weight: 0.1980 chunk 244 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS ** a 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 201 GLN F 66 GLN F 72 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 351 ASN B 210 ASN B 310 GLN B 325 GLN e 30 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 134 ASN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN ** R 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN d 206 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.7931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39778 Z= 0.206 Angle : 0.698 10.348 53943 Z= 0.348 Chirality : 0.045 0.616 6456 Planarity : 0.005 0.073 6961 Dihedral : 5.747 69.907 5682 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.34 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 5149 helix: 0.50 (0.10), residues: 2842 sheet: -0.66 (0.20), residues: 621 loop : -0.50 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 117 HIS 0.007 0.001 HIS d 190 PHE 0.029 0.002 PHE g 255 TYR 0.052 0.001 TYR a 74 ARG 0.011 0.001 ARG P 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10298 Ramachandran restraints generated. 5149 Oldfield, 0 Emsley, 5149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 860 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 174 ILE cc_start: 0.7962 (pt) cc_final: 0.7745 (tp) REVERT: a 184 LEU cc_start: 0.8123 (tp) cc_final: 0.7344 (tp) REVERT: a 222 PHE cc_start: 0.8121 (t80) cc_final: 0.7395 (t80) REVERT: C 82 MET cc_start: 0.8064 (tpp) cc_final: 0.7755 (tpp) REVERT: C 219 MET cc_start: 0.8815 (mmp) cc_final: 0.8370 (mmp) REVERT: C 223 ILE cc_start: 0.9224 (mp) cc_final: 0.8655 (tt) REVERT: C 287 TYR cc_start: 0.8361 (m-80) cc_final: 0.7977 (m-80) REVERT: C 290 ASP cc_start: 0.8152 (m-30) cc_final: 0.7763 (t0) REVERT: C 298 LEU cc_start: 0.9280 (tp) cc_final: 0.9004 (tp) REVERT: C 480 LYS cc_start: 0.8791 (mttt) cc_final: 0.8479 (ptmt) REVERT: C 487 GLU cc_start: 0.8163 (pp20) cc_final: 0.7826 (pp20) REVERT: C 498 MET cc_start: 0.7790 (ttm) cc_final: 0.6805 (tpt) REVERT: D 247 MET cc_start: 0.8129 (mmm) cc_final: 0.7907 (mmm) REVERT: D 280 GLN cc_start: 0.8883 (pp30) cc_final: 0.8103 (pp30) REVERT: D 336 ASP cc_start: 0.9361 (t0) cc_final: 0.9029 (t0) REVERT: D 351 VAL cc_start: 0.9002 (t) cc_final: 0.8739 (p) REVERT: D 428 GLU cc_start: 0.8724 (pt0) cc_final: 0.8249 (pt0) REVERT: D 475 TYR cc_start: 0.8080 (t80) cc_final: 0.7815 (t80) REVERT: D 481 ASP cc_start: 0.8993 (m-30) cc_final: 0.8508 (p0) REVERT: E 18 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8348 (mm-30) REVERT: E 55 GLU cc_start: 0.8406 (tp30) cc_final: 0.8100 (tp30) REVERT: E 66 ASN cc_start: 0.8920 (m110) cc_final: 0.8402 (t0) REVERT: E 74 VAL cc_start: 0.9168 (t) cc_final: 0.8882 (p) REVERT: E 131 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 157 MET cc_start: 0.7583 (mpp) cc_final: 0.7020 (mpp) REVERT: E 241 TYR cc_start: 0.9149 (m-80) cc_final: 0.8920 (m-10) REVERT: E 251 MET cc_start: 0.8401 (ttt) cc_final: 0.7302 (tpp) REVERT: E 258 LEU cc_start: 0.9394 (tp) cc_final: 0.9129 (tp) REVERT: E 340 ASP cc_start: 0.8208 (m-30) cc_final: 0.7891 (m-30) REVERT: E 342 GLN cc_start: 0.8576 (pm20) cc_final: 0.7700 (pp30) REVERT: E 376 MET cc_start: 0.7375 (mmt) cc_final: 0.6767 (mmt) REVERT: E 436 MET cc_start: 0.7334 (ppp) cc_final: 0.7029 (ppp) REVERT: E 497 GLN cc_start: 0.6004 (tp40) cc_final: 0.5601 (tp40) REVERT: F 39 LYS cc_start: 0.8914 (mppt) cc_final: 0.8533 (mttt) REVERT: F 59 MET cc_start: 0.6205 (tpp) cc_final: 0.5932 (tmm) REVERT: F 79 MET cc_start: 0.9186 (mmt) cc_final: 0.8961 (mmt) REVERT: F 112 ASN cc_start: 0.8609 (m110) cc_final: 0.8185 (m110) REVERT: F 184 GLU cc_start: 0.8342 (tp30) cc_final: 0.8109 (tp30) REVERT: F 254 LEU cc_start: 0.9038 (tp) cc_final: 0.8714 (tp) REVERT: F 292 MET cc_start: 0.9139 (mtt) cc_final: 0.8781 (mtt) REVERT: F 419 LEU cc_start: 0.8571 (tt) cc_final: 0.8299 (mt) REVERT: F 477 VAL cc_start: 0.9289 (m) cc_final: 0.8973 (p) REVERT: A 37 ASP cc_start: 0.7535 (t0) cc_final: 0.7235 (t0) REVERT: A 140 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8096 (mtt-85) REVERT: A 157 MET cc_start: 0.8603 (mpp) cc_final: 0.8016 (mpp) REVERT: A 267 GLN cc_start: 0.9184 (tt0) cc_final: 0.8677 (tm-30) REVERT: A 290 ASP cc_start: 0.7723 (p0) cc_final: 0.7508 (p0) REVERT: A 296 SER cc_start: 0.9322 (p) cc_final: 0.9010 (t) REVERT: A 338 ILE cc_start: 0.9488 (tp) cc_final: 0.8949 (tt) REVERT: A 382 LYS cc_start: 0.8523 (mttt) cc_final: 0.8042 (mmmm) REVERT: A 436 MET cc_start: 0.8087 (ppp) cc_final: 0.7177 (ppp) REVERT: A 458 LEU cc_start: 0.8968 (tp) cc_final: 0.8676 (tp) REVERT: A 499 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7697 (mm-30) REVERT: B 79 MET cc_start: 0.8608 (mmm) cc_final: 0.8078 (mmm) REVERT: B 168 ILE cc_start: 0.9467 (mm) cc_final: 0.9026 (mm) REVERT: B 204 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6175 (mm-30) REVERT: B 274 ASN cc_start: 0.8576 (t0) cc_final: 0.8135 (t0) REVERT: B 370 SER cc_start: 0.9604 (m) cc_final: 0.9030 (p) REVERT: B 411 ASP cc_start: 0.7131 (t70) cc_final: 0.6528 (t0) REVERT: B 435 PHE cc_start: 0.8495 (m-80) cc_final: 0.7746 (m-80) REVERT: B 475 TYR cc_start: 0.9037 (t80) cc_final: 0.8652 (t80) REVERT: B 476 LEU cc_start: 0.8669 (mt) cc_final: 0.8069 (mt) REVERT: e 94 GLN cc_start: 0.9047 (tt0) cc_final: 0.8466 (mt0) REVERT: e 111 GLN cc_start: 0.8805 (tt0) cc_final: 0.8287 (mp10) REVERT: e 112 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7684 (pttp) REVERT: g 135 ASN cc_start: 0.8777 (m-40) cc_final: 0.8231 (t0) REVERT: g 136 MET cc_start: 0.8232 (tpp) cc_final: 0.7656 (tpp) REVERT: g 144 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8451 (mmm160) REVERT: g 163 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7180 (tppt) REVERT: g 173 GLU cc_start: 0.7815 (pp20) cc_final: 0.7463 (pp20) REVERT: g 192 GLN cc_start: 0.8262 (tp40) cc_final: 0.7061 (tp40) REVERT: g 196 ASP cc_start: 0.8301 (m-30) cc_final: 0.7843 (m-30) REVERT: g 287 ASP cc_start: 0.8252 (t70) cc_final: 0.7993 (t70) REVERT: g 315 GLU cc_start: 0.8852 (tt0) cc_final: 0.8012 (tm-30) REVERT: S 34 GLN cc_start: 0.5750 (tt0) cc_final: 0.5419 (tt0) REVERT: S 36 VAL cc_start: 0.6612 (t) cc_final: 0.6390 (t) REVERT: S 75 LEU cc_start: 0.7410 (tp) cc_final: 0.6436 (mm) REVERT: O 68 LEU cc_start: 0.6913 (tp) cc_final: 0.6213 (tp) REVERT: T 60 MET cc_start: 0.5595 (mmm) cc_final: 0.5088 (mmm) REVERT: G 60 MET cc_start: 0.4903 (ttt) cc_final: 0.4257 (ttt) REVERT: H 49 ILE cc_start: 0.7962 (mt) cc_final: 0.7677 (mt) REVERT: K 60 MET cc_start: 0.5692 (tpt) cc_final: 0.4702 (ttp) REVERT: J 28 GLN cc_start: 0.6549 (mt0) cc_final: 0.5491 (tt0) REVERT: I 50 ARG cc_start: 0.8026 (ttp80) cc_final: 0.7014 (ttp-170) REVERT: I 60 MET cc_start: 0.3600 (mmm) cc_final: 0.3080 (mtp) REVERT: p 102 PHE cc_start: 0.3201 (m-80) cc_final: 0.2937 (m-80) REVERT: b 90 MET cc_start: 0.6912 (ppp) cc_final: 0.6649 (ppp) REVERT: b 179 MET cc_start: 0.5696 (ppp) cc_final: 0.5269 (ppp) REVERT: d 243 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9036 (tm-30) outliers start: 2 outliers final: 0 residues processed: 861 average time/residue: 0.4953 time to fit residues: 715.3095 Evaluate side-chains 644 residues out of total 4106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 316 optimal weight: 0.0470 chunk 425 optimal weight: 0.7980 chunk 122 optimal weight: 0.0020 chunk 367 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.0670 chunk 399 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 24 GLN a 25 HIS ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 ASN E 201 GLN F 72 ASN F 310 GLN F 325 GLN A 173 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN e 30 GLN ** g 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.133339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107689 restraints weight = 98586.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105109 restraints weight = 96095.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105953 restraints weight = 78704.213| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.8094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39778 Z= 0.186 Angle : 0.672 14.593 53943 Z= 0.335 Chirality : 0.043 0.226 6456 Planarity : 0.005 0.078 6961 Dihedral : 5.542 66.573 5682 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5149 helix: 0.63 (0.10), residues: 2795 sheet: -0.61 (0.21), residues: 602 loop : -0.56 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 117 HIS 0.003 0.001 HIS e 37 PHE 0.034 0.002 PHE a 78 TYR 0.017 0.001 TYR a 148 ARG 0.009 0.001 ARG I 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12298.82 seconds wall clock time: 219 minutes 18.94 seconds (13158.94 seconds total)