Starting phenix.real_space_refine on Tue Feb 13 05:13:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgz_40474/02_2024/8sgz_40474_updated.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 354 5.16 5 C 33684 2.51 5 N 9342 2.21 5 O 10050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 16": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B GLU 547": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Residue "F GLU 51": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H GLU 290": "OE1" <-> "OE2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S GLU 62": "OE1" <-> "OE2" Residue "S ARG 296": "NH1" <-> "NH2" Residue "S GLU 300": "OE1" <-> "OE2" Residue "S GLU 402": "OE1" <-> "OE2" Residue "S ARG 406": "NH1" <-> "NH2" Residue "S GLU 547": "OE1" <-> "OE2" Residue "S GLU 549": "OE1" <-> "OE2" Residue "S GLU 622": "OE1" <-> "OE2" Residue "S GLU 623": "OE1" <-> "OE2" Residue "S GLU 628": "OE1" <-> "OE2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V GLU 62": "OE1" <-> "OE2" Residue "V ARG 296": "NH1" <-> "NH2" Residue "V GLU 300": "OE1" <-> "OE2" Residue "V GLU 402": "OE1" <-> "OE2" Residue "V ARG 406": "NH1" <-> "NH2" Residue "V GLU 547": "OE1" <-> "OE2" Residue "V GLU 549": "OE1" <-> "OE2" Residue "V GLU 622": "OE1" <-> "OE2" Residue "V GLU 623": "OE1" <-> "OE2" Residue "V GLU 628": "OE1" <-> "OE2" Residue "X GLU 16": "OE1" <-> "OE2" Residue "X GLU 62": "OE1" <-> "OE2" Residue "X ARG 296": "NH1" <-> "NH2" Residue "X GLU 300": "OE1" <-> "OE2" Residue "X GLU 402": "OE1" <-> "OE2" Residue "X ARG 406": "NH1" <-> "NH2" Residue "X GLU 547": "OE1" <-> "OE2" Residue "X GLU 549": "OE1" <-> "OE2" Residue "X GLU 622": "OE1" <-> "OE2" Residue "X GLU 623": "OE1" <-> "OE2" Residue "X GLU 628": "OE1" <-> "OE2" Residue "Z GLU 16": "OE1" <-> "OE2" Residue "Z GLU 62": "OE1" <-> "OE2" Residue "Z ARG 296": "NH1" <-> "NH2" Residue "Z GLU 300": "OE1" <-> "OE2" Residue "Z GLU 402": "OE1" <-> "OE2" Residue "Z ARG 406": "NH1" <-> "NH2" Residue "Z GLU 547": "OE1" <-> "OE2" Residue "Z GLU 549": "OE1" <-> "OE2" Residue "Z GLU 622": "OE1" <-> "OE2" Residue "Z GLU 623": "OE1" <-> "OE2" Residue "Z GLU 628": "OE1" <-> "OE2" Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y GLU 62": "OE1" <-> "OE2" Residue "Y ARG 296": "NH1" <-> "NH2" Residue "Y GLU 300": "OE1" <-> "OE2" Residue "Y GLU 402": "OE1" <-> "OE2" Residue "Y ARG 406": "NH1" <-> "NH2" Residue "Y GLU 547": "OE1" <-> "OE2" Residue "Y GLU 549": "OE1" <-> "OE2" Residue "Y GLU 622": "OE1" <-> "OE2" Residue "Y GLU 623": "OE1" <-> "OE2" Residue "Y GLU 628": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 53430 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "C" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "D" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "E" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "F" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "G" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "H" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3766 Classifications: {'peptide': 489} Link IDs: {'PTRANS': 27, 'TRANS': 461} Chain: "S" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "V" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "X" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "Z" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "Y" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5124 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 26, 'TRANS': 630} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.87, per 1000 atoms: 0.37 Number of scatterers: 53430 At special positions: 0 Unit cell: (182.6, 199.1, 183.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 354 16.00 O 10050 8.00 N 9342 7.00 C 33684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.73 Conformation dependent library (CDL) restraints added in 7.0 seconds 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 234 helices and 54 sheets defined 32.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.16 Creating SS restraints... Processing helix chain 'B' and resid 16 through 28 removed outlier: 4.611A pdb=" N ARG B 26 " --> pdb=" O MET B 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 93 through 101 removed outlier: 3.540A pdb=" N ALA B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.855A pdb=" N ILE B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 4.056A pdb=" N ALA B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.631A pdb=" N ASP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 460 through 481 removed outlier: 3.630A pdb=" N LEU B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 584 Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 118 through 131 removed outlier: 3.687A pdb=" N VAL C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 167 removed outlier: 7.213A pdb=" N VAL C 151 " --> pdb=" O HIS C 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 152 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 153 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 167 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 removed outlier: 3.663A pdb=" N VAL C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER C 188 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Proline residue: C 189 - end of helix Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.567A pdb=" N ARG C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 285 Processing helix chain 'C' and resid 297 through 304 removed outlier: 4.812A pdb=" N TYR C 302 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.556A pdb=" N PHE C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.573A pdb=" N ALA C 394 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU C 396 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 397 " --> pdb=" O GLY C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.762A pdb=" N ASP C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 453 Processing helix chain 'C' and resid 461 through 473 removed outlier: 4.090A pdb=" N ALA C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 491 through 507 removed outlier: 3.910A pdb=" N THR C 494 " --> pdb=" O PRO C 491 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG C 495 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 505 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 506 " --> pdb=" O GLU C 503 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 507 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.688A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 167 removed outlier: 7.212A pdb=" N VAL D 151 " --> pdb=" O HIS D 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 152 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 153 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 167 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.662A pdb=" N VAL D 186 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 188 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Proline residue: D 189 - end of helix Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.568A pdb=" N ARG D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 297 through 304 removed outlier: 4.811A pdb=" N TYR D 302 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.555A pdb=" N PHE D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 386 Processing helix chain 'D' and resid 389 through 402 removed outlier: 3.574A pdb=" N ALA D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU D 396 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 397 " --> pdb=" O GLY D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.762A pdb=" N ASP D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 453 Processing helix chain 'D' and resid 461 through 473 removed outlier: 4.090A pdb=" N ALA D 467 " --> pdb=" O ALA D 463 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP D 468 " --> pdb=" O GLN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 482 Processing helix chain 'D' and resid 491 through 507 removed outlier: 3.910A pdb=" N THR D 494 " --> pdb=" O PRO D 491 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG D 495 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 505 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 506 " --> pdb=" O GLU D 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG D 507 " --> pdb=" O ARG D 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 118 through 131 removed outlier: 3.688A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 167 removed outlier: 7.211A pdb=" N VAL E 151 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP E 152 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER E 153 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE E 167 " --> pdb=" O ASN E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 removed outlier: 3.663A pdb=" N VAL E 186 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER E 188 " --> pdb=" O ALA E 185 " (cutoff:3.500A) Proline residue: E 189 - end of helix Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 228 through 233 Processing helix chain 'E' and resid 245 through 258 removed outlier: 3.567A pdb=" N ARG E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 285 Processing helix chain 'E' and resid 297 through 304 removed outlier: 4.811A pdb=" N TYR E 302 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'E' and resid 349 through 365 removed outlier: 3.556A pdb=" N PHE E 365 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.573A pdb=" N ALA E 394 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU E 396 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 397 " --> pdb=" O GLY E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.761A pdb=" N ASP E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 453 Processing helix chain 'E' and resid 461 through 473 removed outlier: 4.090A pdb=" N ALA E 467 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP E 468 " --> pdb=" O GLN E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 491 through 507 removed outlier: 3.911A pdb=" N THR E 494 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG E 495 " --> pdb=" O SER E 492 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 505 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 506 " --> pdb=" O GLU E 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E 507 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 56 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 118 through 131 removed outlier: 3.688A pdb=" N VAL F 122 " --> pdb=" O ASN F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 167 removed outlier: 7.212A pdb=" N VAL F 151 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP F 152 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 153 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE F 167 " --> pdb=" O ASN F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.663A pdb=" N VAL F 186 " --> pdb=" O GLY F 183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 188 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'F' and resid 245 through 258 removed outlier: 3.568A pdb=" N ARG F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 285 Processing helix chain 'F' and resid 297 through 304 removed outlier: 4.812A pdb=" N TYR F 302 " --> pdb=" O ASP F 299 " (cutoff:3.500A) Proline residue: F 303 - end of helix Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 349 through 365 removed outlier: 3.555A pdb=" N PHE F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 386 Processing helix chain 'F' and resid 389 through 402 removed outlier: 3.573A pdb=" N ALA F 394 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS F 395 " --> pdb=" O ARG F 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU F 396 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 397 " --> pdb=" O GLY F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 3.762A pdb=" N ASP F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 453 Processing helix chain 'F' and resid 461 through 473 removed outlier: 4.091A pdb=" N ALA F 467 " --> pdb=" O ALA F 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP F 468 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 491 through 507 removed outlier: 3.909A pdb=" N THR F 494 " --> pdb=" O PRO F 491 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG F 495 " --> pdb=" O SER F 492 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 505 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 506 " --> pdb=" O GLU F 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG F 507 " --> pdb=" O ARG F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS G 44 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 118 through 131 removed outlier: 3.687A pdb=" N VAL G 122 " --> pdb=" O ASN G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 167 removed outlier: 7.213A pdb=" N VAL G 151 " --> pdb=" O HIS G 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP G 152 " --> pdb=" O GLU G 149 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 153 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE G 167 " --> pdb=" O ASN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 191 removed outlier: 3.663A pdb=" N VAL G 186 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER G 188 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Proline residue: G 189 - end of helix Processing helix chain 'G' and resid 209 through 215 Processing helix chain 'G' and resid 222 through 226 Processing helix chain 'G' and resid 228 through 233 Processing helix chain 'G' and resid 245 through 258 removed outlier: 3.567A pdb=" N ARG G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 285 Processing helix chain 'G' and resid 297 through 304 removed outlier: 4.812A pdb=" N TYR G 302 " --> pdb=" O ASP G 299 " (cutoff:3.500A) Proline residue: G 303 - end of helix Processing helix chain 'G' and resid 343 through 345 No H-bonds generated for 'chain 'G' and resid 343 through 345' Processing helix chain 'G' and resid 349 through 365 removed outlier: 3.554A pdb=" N PHE G 365 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 386 Processing helix chain 'G' and resid 389 through 402 removed outlier: 3.573A pdb=" N ALA G 394 " --> pdb=" O ILE G 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS G 395 " --> pdb=" O ARG G 391 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU G 396 " --> pdb=" O HIS G 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 397 " --> pdb=" O GLY G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 422 removed outlier: 3.763A pdb=" N ASP G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 453 Processing helix chain 'G' and resid 461 through 473 removed outlier: 4.090A pdb=" N ALA G 467 " --> pdb=" O ALA G 463 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP G 468 " --> pdb=" O GLN G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 482 Processing helix chain 'G' and resid 491 through 507 removed outlier: 3.911A pdb=" N THR G 494 " --> pdb=" O PRO G 491 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG G 495 " --> pdb=" O SER G 492 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU G 505 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 506 " --> pdb=" O GLU G 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG G 507 " --> pdb=" O ARG G 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.997A pdb=" N LYS H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 118 through 131 removed outlier: 3.687A pdb=" N VAL H 122 " --> pdb=" O ASN H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 167 removed outlier: 7.213A pdb=" N VAL H 151 " --> pdb=" O HIS H 148 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP H 152 " --> pdb=" O GLU H 149 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER H 153 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE H 167 " --> pdb=" O ASN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.663A pdb=" N VAL H 186 " --> pdb=" O GLY H 183 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER H 188 " --> pdb=" O ALA H 185 " (cutoff:3.500A) Proline residue: H 189 - end of helix Processing helix chain 'H' and resid 209 through 215 Processing helix chain 'H' and resid 222 through 226 Processing helix chain 'H' and resid 228 through 233 Processing helix chain 'H' and resid 245 through 258 removed outlier: 3.567A pdb=" N ARG H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 285 Processing helix chain 'H' and resid 297 through 304 removed outlier: 4.812A pdb=" N TYR H 302 " --> pdb=" O ASP H 299 " (cutoff:3.500A) Proline residue: H 303 - end of helix Processing helix chain 'H' and resid 343 through 345 No H-bonds generated for 'chain 'H' and resid 343 through 345' Processing helix chain 'H' and resid 349 through 365 removed outlier: 3.555A pdb=" N PHE H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 386 Processing helix chain 'H' and resid 389 through 402 removed outlier: 3.573A pdb=" N ALA H 394 " --> pdb=" O ILE H 390 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS H 395 " --> pdb=" O ARG H 391 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 396 " --> pdb=" O HIS H 392 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU H 397 " --> pdb=" O GLY H 393 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 422 removed outlier: 3.762A pdb=" N ASP H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 453 Processing helix chain 'H' and resid 461 through 473 removed outlier: 4.090A pdb=" N ALA H 467 " --> pdb=" O ALA H 463 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP H 468 " --> pdb=" O GLN H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 482 Processing helix chain 'H' and resid 491 through 507 removed outlier: 3.910A pdb=" N THR H 494 " --> pdb=" O PRO H 491 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG H 495 " --> pdb=" O SER H 492 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU H 505 " --> pdb=" O LEU H 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA H 506 " --> pdb=" O GLU H 503 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG H 507 " --> pdb=" O ARG H 504 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 28 removed outlier: 4.611A pdb=" N ARG S 26 " --> pdb=" O MET S 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG S 27 " --> pdb=" O ALA S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 40 No H-bonds generated for 'chain 'S' and resid 38 through 40' Processing helix chain 'S' and resid 44 through 48 Processing helix chain 'S' and resid 67 through 73 Processing helix chain 'S' and resid 93 through 101 removed outlier: 3.541A pdb=" N ALA S 98 " --> pdb=" O GLU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 117 Processing helix chain 'S' and resid 123 through 129 Processing helix chain 'S' and resid 145 through 155 removed outlier: 3.855A pdb=" N ILE S 155 " --> pdb=" O PHE S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA S 194 " --> pdb=" O GLU S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 253 through 269 removed outlier: 4.056A pdb=" N ALA S 258 " --> pdb=" O THR S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 307 Processing helix chain 'S' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA S 321 " --> pdb=" O LEU S 317 " (cutoff:3.500A) Processing helix chain 'S' and resid 400 through 412 removed outlier: 3.630A pdb=" N ASP S 412 " --> pdb=" O GLU S 408 " (cutoff:3.500A) Processing helix chain 'S' and resid 423 through 431 Processing helix chain 'S' and resid 433 through 437 Processing helix chain 'S' and resid 444 through 448 Processing helix chain 'S' and resid 460 through 481 removed outlier: 3.629A pdb=" N LEU S 480 " --> pdb=" O LYS S 476 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS S 481 " --> pdb=" O ARG S 477 " (cutoff:3.500A) Processing helix chain 'S' and resid 578 through 584 Processing helix chain 'V' and resid 16 through 28 removed outlier: 4.611A pdb=" N ARG V 26 " --> pdb=" O MET V 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG V 27 " --> pdb=" O ALA V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 40 No H-bonds generated for 'chain 'V' and resid 38 through 40' Processing helix chain 'V' and resid 44 through 48 Processing helix chain 'V' and resid 67 through 73 Processing helix chain 'V' and resid 93 through 101 removed outlier: 3.540A pdb=" N ALA V 98 " --> pdb=" O GLU V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 117 Processing helix chain 'V' and resid 123 through 129 Processing helix chain 'V' and resid 145 through 155 removed outlier: 3.854A pdb=" N ILE V 155 " --> pdb=" O PHE V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA V 194 " --> pdb=" O GLU V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 253 through 269 removed outlier: 4.056A pdb=" N ALA V 258 " --> pdb=" O THR V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 307 Processing helix chain 'V' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA V 321 " --> pdb=" O LEU V 317 " (cutoff:3.500A) Processing helix chain 'V' and resid 400 through 412 removed outlier: 3.631A pdb=" N ASP V 412 " --> pdb=" O GLU V 408 " (cutoff:3.500A) Processing helix chain 'V' and resid 423 through 431 Processing helix chain 'V' and resid 433 through 437 Processing helix chain 'V' and resid 444 through 448 Processing helix chain 'V' and resid 460 through 481 removed outlier: 3.629A pdb=" N LEU V 480 " --> pdb=" O LYS V 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS V 481 " --> pdb=" O ARG V 477 " (cutoff:3.500A) Processing helix chain 'V' and resid 578 through 584 Processing helix chain 'X' and resid 16 through 28 removed outlier: 4.611A pdb=" N ARG X 26 " --> pdb=" O MET X 22 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 40 No H-bonds generated for 'chain 'X' and resid 38 through 40' Processing helix chain 'X' and resid 44 through 48 Processing helix chain 'X' and resid 67 through 73 Processing helix chain 'X' and resid 93 through 101 removed outlier: 3.540A pdb=" N ALA X 98 " --> pdb=" O GLU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 117 Processing helix chain 'X' and resid 123 through 129 Processing helix chain 'X' and resid 145 through 155 removed outlier: 3.855A pdb=" N ILE X 155 " --> pdb=" O PHE X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA X 194 " --> pdb=" O GLU X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 253 through 269 removed outlier: 4.055A pdb=" N ALA X 258 " --> pdb=" O THR X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 307 Processing helix chain 'X' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA X 321 " --> pdb=" O LEU X 317 " (cutoff:3.500A) Processing helix chain 'X' and resid 400 through 412 removed outlier: 3.630A pdb=" N ASP X 412 " --> pdb=" O GLU X 408 " (cutoff:3.500A) Processing helix chain 'X' and resid 423 through 431 Processing helix chain 'X' and resid 433 through 437 Processing helix chain 'X' and resid 444 through 448 Processing helix chain 'X' and resid 460 through 481 removed outlier: 3.629A pdb=" N LEU X 480 " --> pdb=" O LYS X 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS X 481 " --> pdb=" O ARG X 477 " (cutoff:3.500A) Processing helix chain 'X' and resid 578 through 584 Processing helix chain 'Z' and resid 16 through 28 removed outlier: 4.611A pdb=" N ARG Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 40 No H-bonds generated for 'chain 'Z' and resid 38 through 40' Processing helix chain 'Z' and resid 44 through 48 Processing helix chain 'Z' and resid 67 through 73 Processing helix chain 'Z' and resid 93 through 101 removed outlier: 3.538A pdb=" N ALA Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 117 Processing helix chain 'Z' and resid 123 through 129 Processing helix chain 'Z' and resid 145 through 155 removed outlier: 3.855A pdb=" N ILE Z 155 " --> pdb=" O PHE Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA Z 194 " --> pdb=" O GLU Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 269 removed outlier: 4.056A pdb=" N ALA Z 258 " --> pdb=" O THR Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 301 through 307 Processing helix chain 'Z' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA Z 321 " --> pdb=" O LEU Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 400 through 412 removed outlier: 3.630A pdb=" N ASP Z 412 " --> pdb=" O GLU Z 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 423 through 431 Processing helix chain 'Z' and resid 433 through 437 Processing helix chain 'Z' and resid 444 through 448 Processing helix chain 'Z' and resid 460 through 481 removed outlier: 3.629A pdb=" N LEU Z 480 " --> pdb=" O LYS Z 476 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS Z 481 " --> pdb=" O ARG Z 477 " (cutoff:3.500A) Processing helix chain 'Z' and resid 578 through 584 Processing helix chain 'Y' and resid 16 through 28 removed outlier: 4.609A pdb=" N ARG Y 26 " --> pdb=" O MET Y 22 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 40 No H-bonds generated for 'chain 'Y' and resid 38 through 40' Processing helix chain 'Y' and resid 44 through 48 Processing helix chain 'Y' and resid 67 through 73 Processing helix chain 'Y' and resid 93 through 101 removed outlier: 3.540A pdb=" N ALA Y 98 " --> pdb=" O GLU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 117 Processing helix chain 'Y' and resid 123 through 129 Processing helix chain 'Y' and resid 145 through 155 removed outlier: 3.854A pdb=" N ILE Y 155 " --> pdb=" O PHE Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 178 through 195 removed outlier: 3.560A pdb=" N ALA Y 194 " --> pdb=" O GLU Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 269 removed outlier: 4.057A pdb=" N ALA Y 258 " --> pdb=" O THR Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 301 through 307 Processing helix chain 'Y' and resid 312 through 321 removed outlier: 3.806A pdb=" N ALA Y 321 " --> pdb=" O LEU Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 400 through 412 removed outlier: 3.630A pdb=" N ASP Y 412 " --> pdb=" O GLU Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 423 through 431 Processing helix chain 'Y' and resid 433 through 437 Processing helix chain 'Y' and resid 444 through 448 Processing helix chain 'Y' and resid 460 through 481 removed outlier: 3.629A pdb=" N LEU Y 480 " --> pdb=" O LYS Y 476 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS Y 481 " --> pdb=" O ARG Y 477 " (cutoff:3.500A) Processing helix chain 'Y' and resid 578 through 584 Processing sheet with id= A, first strand: chain 'B' and resid 33 through 36 removed outlier: 5.907A pdb=" N GLU B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR B 36 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL B 53 " --> pdb=" O TYR B 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 214 through 216 Processing sheet with id= C, first strand: chain 'B' and resid 243 through 245 removed outlier: 3.708A pdb=" N CYS B 391 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG B 491 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 509 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 540 through 545 removed outlier: 6.667A pdb=" N GLY B 563 " --> pdb=" O TRP B 555 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR B 557 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B 561 " --> pdb=" O THR B 557 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 606 through 610 removed outlier: 6.895A pdb=" N THR B 626 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU C 102 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE C 194 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE C 177 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE C 196 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY C 240 " --> pdb=" O MET C 197 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS C 323 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C 336 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 370 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASN C 338 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE C 372 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER C 432 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE C 411 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR C 434 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 487 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 414 through 416 removed outlier: 6.613A pdb=" N GLU C 440 " --> pdb=" O ALA C 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU D 102 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE D 194 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 177 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE D 196 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY D 240 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS D 323 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE D 336 " --> pdb=" O PRO D 368 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 370 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASN D 338 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE D 372 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 432 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE D 411 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR D 434 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA D 487 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 414 through 416 removed outlier: 6.613A pdb=" N GLU D 440 " --> pdb=" O ALA D 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU E 102 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE E 194 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE E 177 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE E 196 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 240 " --> pdb=" O MET E 197 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 310 through 313 removed outlier: 4.635A pdb=" N CYS E 323 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 336 " --> pdb=" O PRO E 368 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE E 370 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ASN E 338 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE E 372 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER E 432 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE E 411 " --> pdb=" O SER E 432 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR E 434 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 487 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 414 through 416 removed outlier: 6.613A pdb=" N GLU E 440 " --> pdb=" O ALA E 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'F' and resid 88 through 91 removed outlier: 3.786A pdb=" N LEU F 102 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE F 194 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE F 177 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE F 196 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY F 240 " --> pdb=" O MET F 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS F 323 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE F 336 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 370 " --> pdb=" O ILE F 336 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASN F 338 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE F 372 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER F 432 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE F 411 " --> pdb=" O SER F 432 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR F 434 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA F 487 " --> pdb=" O ALA F 435 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 414 through 416 removed outlier: 6.612A pdb=" N GLU F 440 " --> pdb=" O ALA F 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'G' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU G 102 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE G 194 " --> pdb=" O SER G 175 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE G 177 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE G 196 " --> pdb=" O ILE G 177 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY G 240 " --> pdb=" O MET G 197 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 310 through 313 removed outlier: 4.633A pdb=" N CYS G 323 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE G 336 " --> pdb=" O PRO G 368 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE G 370 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASN G 338 " --> pdb=" O ILE G 370 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE G 372 " --> pdb=" O ASN G 338 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER G 432 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE G 411 " --> pdb=" O SER G 432 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR G 434 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA G 487 " --> pdb=" O ALA G 435 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 414 through 416 removed outlier: 6.613A pdb=" N GLU G 440 " --> pdb=" O ALA G 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'H' and resid 88 through 91 removed outlier: 3.785A pdb=" N LEU H 102 " --> pdb=" O GLY H 91 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE H 194 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE H 177 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE H 196 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY H 240 " --> pdb=" O MET H 197 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 310 through 313 removed outlier: 4.634A pdb=" N CYS H 323 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE H 336 " --> pdb=" O PRO H 368 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE H 370 " --> pdb=" O ILE H 336 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASN H 338 " --> pdb=" O ILE H 370 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE H 372 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER H 432 " --> pdb=" O THR H 409 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE H 411 " --> pdb=" O SER H 432 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR H 434 " --> pdb=" O ILE H 411 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA H 487 " --> pdb=" O ALA H 435 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 414 through 416 removed outlier: 6.614A pdb=" N GLU H 440 " --> pdb=" O ALA H 415 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'S' and resid 33 through 36 removed outlier: 5.906A pdb=" N GLU S 51 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR S 36 " --> pdb=" O GLU S 51 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL S 53 " --> pdb=" O TYR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'S' and resid 214 through 216 Processing sheet with id= AA, first strand: chain 'S' and resid 243 through 245 removed outlier: 3.708A pdb=" N CYS S 391 " --> pdb=" O VAL S 343 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'S' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG S 491 " --> pdb=" O VAL S 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 509 " --> pdb=" O ARG S 491 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 540 through 545 removed outlier: 6.667A pdb=" N GLY S 563 " --> pdb=" O TRP S 555 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR S 557 " --> pdb=" O THR S 561 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR S 561 " --> pdb=" O THR S 557 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'S' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR S 626 " --> pdb=" O VAL S 608 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'V' and resid 33 through 36 removed outlier: 5.907A pdb=" N GLU V 51 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR V 36 " --> pdb=" O GLU V 51 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL V 53 " --> pdb=" O TYR V 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'V' and resid 214 through 216 Processing sheet with id= AG, first strand: chain 'V' and resid 243 through 245 removed outlier: 3.708A pdb=" N CYS V 391 " --> pdb=" O VAL V 343 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG V 491 " --> pdb=" O VAL V 509 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL V 509 " --> pdb=" O ARG V 491 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'V' and resid 540 through 545 removed outlier: 6.667A pdb=" N GLY V 563 " --> pdb=" O TRP V 555 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR V 557 " --> pdb=" O THR V 561 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR V 561 " --> pdb=" O THR V 557 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'V' and resid 606 through 610 removed outlier: 6.895A pdb=" N THR V 626 " --> pdb=" O VAL V 608 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'X' and resid 33 through 36 removed outlier: 5.907A pdb=" N GLU X 51 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TYR X 36 " --> pdb=" O GLU X 51 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL X 53 " --> pdb=" O TYR X 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'X' and resid 277 through 279 removed outlier: 4.008A pdb=" N GLN X 216 " --> pdb=" O LEU X 228 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 243 through 245 removed outlier: 3.707A pdb=" N CYS X 391 " --> pdb=" O VAL X 343 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG X 491 " --> pdb=" O VAL X 509 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL X 509 " --> pdb=" O ARG X 491 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 540 through 545 removed outlier: 6.668A pdb=" N GLY X 563 " --> pdb=" O TRP X 555 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR X 557 " --> pdb=" O THR X 561 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR X 561 " --> pdb=" O THR X 557 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'X' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR X 626 " --> pdb=" O VAL X 608 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Z' and resid 33 through 36 removed outlier: 5.907A pdb=" N GLU Z 51 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TYR Z 36 " --> pdb=" O GLU Z 51 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL Z 53 " --> pdb=" O TYR Z 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'Z' and resid 277 through 279 removed outlier: 4.008A pdb=" N GLN Z 216 " --> pdb=" O LEU Z 228 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Z' and resid 243 through 245 removed outlier: 3.707A pdb=" N CYS Z 391 " --> pdb=" O VAL Z 343 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Z' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG Z 491 " --> pdb=" O VAL Z 509 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Z 509 " --> pdb=" O ARG Z 491 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Z' and resid 540 through 545 removed outlier: 6.667A pdb=" N GLY Z 563 " --> pdb=" O TRP Z 555 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR Z 557 " --> pdb=" O THR Z 561 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR Z 561 " --> pdb=" O THR Z 557 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Z' and resid 606 through 610 removed outlier: 6.896A pdb=" N THR Z 626 " --> pdb=" O VAL Z 608 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Y' and resid 33 through 36 removed outlier: 5.906A pdb=" N GLU Y 51 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR Y 36 " --> pdb=" O GLU Y 51 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL Y 53 " --> pdb=" O TYR Y 36 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'Y' and resid 277 through 279 removed outlier: 4.008A pdb=" N GLN Y 216 " --> pdb=" O LEU Y 228 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Y' and resid 243 through 245 removed outlier: 3.708A pdb=" N CYS Y 391 " --> pdb=" O VAL Y 343 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Y' and resid 491 through 495 removed outlier: 3.598A pdb=" N ARG Y 491 " --> pdb=" O VAL Y 509 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL Y 509 " --> pdb=" O ARG Y 491 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Y' and resid 540 through 545 removed outlier: 6.666A pdb=" N GLY Y 563 " --> pdb=" O TRP Y 555 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR Y 557 " --> pdb=" O THR Y 561 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR Y 561 " --> pdb=" O THR Y 557 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Y' and resid 606 through 610 removed outlier: 6.894A pdb=" N THR Y 626 " --> pdb=" O VAL Y 608 " (cutoff:3.500A) 1461 hydrogen bonds defined for protein. 3780 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: 16.38 Time building geometry restraints manager: 16.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11878 1.33 - 1.45: 11227 1.45 - 1.57: 30805 1.57 - 1.69: 0 1.69 - 1.81: 570 Bond restraints: 54480 Sorted by residual: bond pdb=" C2 BTI H 801 " pdb=" S1 BTI H 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 BTI D 801 " pdb=" S1 BTI D 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C2 BTI C 801 " pdb=" S1 BTI C 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C2 BTI E 801 " pdb=" S1 BTI E 801 " ideal model delta sigma weight residual 1.822 1.758 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C2 BTI G 801 " pdb=" S1 BTI G 801 " ideal model delta sigma weight residual 1.822 1.759 0.063 2.00e-02 2.50e+03 1.00e+01 ... (remaining 54475 not shown) Histogram of bond angle deviations from ideal: 95.57 - 103.26: 541 103.26 - 110.94: 19604 110.94 - 118.63: 23670 118.63 - 126.32: 29289 126.32 - 134.01: 612 Bond angle restraints: 73716 Sorted by residual: angle pdb=" N GLY Z 309 " pdb=" CA GLY Z 309 " pdb=" C GLY Z 309 " ideal model delta sigma weight residual 115.64 107.31 8.33 1.46e+00 4.69e-01 3.26e+01 angle pdb=" N GLY V 309 " pdb=" CA GLY V 309 " pdb=" C GLY V 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.22e+01 angle pdb=" N GLY B 309 " pdb=" CA GLY B 309 " pdb=" C GLY B 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.22e+01 angle pdb=" N GLY S 309 " pdb=" CA GLY S 309 " pdb=" C GLY S 309 " ideal model delta sigma weight residual 115.64 107.36 8.28 1.46e+00 4.69e-01 3.21e+01 angle pdb=" N GLY X 309 " pdb=" CA GLY X 309 " pdb=" C GLY X 309 " ideal model delta sigma weight residual 115.64 107.39 8.25 1.46e+00 4.69e-01 3.20e+01 ... (remaining 73711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 30006 17.64 - 35.29: 2592 35.29 - 52.93: 398 52.93 - 70.58: 90 70.58 - 88.22: 22 Dihedral angle restraints: 33108 sinusoidal: 13332 harmonic: 19776 Sorted by residual: dihedral pdb=" CA THR C 200 " pdb=" C THR C 200 " pdb=" N SER C 201 " pdb=" CA SER C 201 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR D 200 " pdb=" C THR D 200 " pdb=" N SER D 201 " pdb=" CA SER D 201 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR F 200 " pdb=" C THR F 200 " pdb=" N SER F 201 " pdb=" CA SER F 201 " ideal model delta harmonic sigma weight residual 180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 33105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5211 0.035 - 0.071: 1967 0.071 - 0.106: 657 0.106 - 0.142: 370 0.142 - 0.177: 39 Chirality restraints: 8244 Sorted by residual: chirality pdb=" C4 BTI C 801 " pdb=" C2 BTI C 801 " pdb=" C5 BTI C 801 " pdb=" N2 BTI C 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" C4 BTI F 801 " pdb=" C2 BTI F 801 " pdb=" C5 BTI F 801 " pdb=" N2 BTI F 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C4 BTI G 801 " pdb=" C2 BTI G 801 " pdb=" C5 BTI G 801 " pdb=" N2 BTI G 801 " both_signs ideal model delta sigma weight residual False 2.75 2.58 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 8241 not shown) Planarity restraints: 9630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI C 801 " -0.009 2.00e-02 2.50e+03 2.02e-02 6.13e+00 pdb=" C4 BTI C 801 " 0.002 2.00e-02 2.50e+03 pdb=" C5 BTI C 801 " 0.027 2.00e-02 2.50e+03 pdb=" N2 BTI C 801 " -0.013 2.00e-02 2.50e+03 pdb=" N3 BTI C 801 " -0.030 2.00e-02 2.50e+03 pdb=" O3 BTI C 801 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 801 " 0.009 2.00e-02 2.50e+03 2.01e-02 6.08e+00 pdb=" C4 BTI G 801 " -0.002 2.00e-02 2.50e+03 pdb=" C5 BTI G 801 " -0.026 2.00e-02 2.50e+03 pdb=" N2 BTI G 801 " 0.014 2.00e-02 2.50e+03 pdb=" N3 BTI G 801 " 0.030 2.00e-02 2.50e+03 pdb=" O3 BTI G 801 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI D 801 " -0.009 2.00e-02 2.50e+03 2.01e-02 6.07e+00 pdb=" C4 BTI D 801 " 0.002 2.00e-02 2.50e+03 pdb=" C5 BTI D 801 " 0.026 2.00e-02 2.50e+03 pdb=" N2 BTI D 801 " -0.014 2.00e-02 2.50e+03 pdb=" N3 BTI D 801 " -0.030 2.00e-02 2.50e+03 pdb=" O3 BTI D 801 " 0.024 2.00e-02 2.50e+03 ... (remaining 9627 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 2026 2.70 - 3.25: 54921 3.25 - 3.80: 82238 3.80 - 4.35: 105754 4.35 - 4.90: 177778 Nonbonded interactions: 422717 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 646 " pdb=" NZ LYS Y 648 " model vdw 2.154 2.520 nonbonded pdb=" OE2 GLU Z 646 " pdb=" NZ LYS Z 648 " model vdw 2.154 2.520 nonbonded pdb=" OE2 GLU X 646 " pdb=" NZ LYS X 648 " model vdw 2.155 2.520 nonbonded pdb=" OE2 GLU V 646 " pdb=" NZ LYS V 648 " model vdw 2.155 2.520 nonbonded pdb=" OE2 GLU S 646 " pdb=" NZ LYS S 648 " model vdw 2.155 2.520 ... (remaining 422712 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 'B' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.050 Extract box with map and model: 13.320 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 100.920 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.340 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.004 0.064 54480 Z= 0.296 Angle : 0.786 8.501 73716 Z= 0.470 Chirality : 0.046 0.177 8244 Planarity : 0.005 0.051 9630 Dihedral : 13.298 88.222 20448 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 1.21 % Allowed : 2.75 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 6852 helix: 0.32 (0.12), residues: 2130 sheet: -0.12 (0.19), residues: 840 loop : -2.18 (0.09), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 514 HIS 0.004 0.001 HIS Z 209 PHE 0.008 0.001 PHE E 62 TYR 0.011 0.001 TYR S 289 ARG 0.005 0.000 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 904 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.4588 (mtm) cc_final: 0.4211 (mmm) REVERT: B 129 ARG cc_start: 0.6194 (tmt170) cc_final: 0.5246 (ttp-170) REVERT: B 259 MET cc_start: 0.3725 (mmp) cc_final: 0.3219 (mmt) REVERT: B 363 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: B 545 ASP cc_start: 0.6547 (t0) cc_final: 0.6110 (p0) REVERT: D 197 MET cc_start: 0.8776 (mtp) cc_final: 0.8559 (mtp) REVERT: S 117 MET cc_start: 0.4603 (mtm) cc_final: 0.4336 (mmm) REVERT: S 129 ARG cc_start: 0.6014 (tmt170) cc_final: 0.5199 (ttp-170) REVERT: S 259 MET cc_start: 0.3652 (mmp) cc_final: 0.3087 (mmt) REVERT: S 444 TYR cc_start: 0.6346 (t80) cc_final: 0.6045 (t80) REVERT: S 545 ASP cc_start: 0.6711 (t0) cc_final: 0.6122 (p0) REVERT: V 117 MET cc_start: 0.4593 (mtm) cc_final: 0.4214 (mmm) REVERT: V 129 ARG cc_start: 0.6215 (tmt170) cc_final: 0.5269 (ttp-170) REVERT: V 259 MET cc_start: 0.3867 (mmp) cc_final: 0.3199 (mmt) REVERT: V 363 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6759 (pt0) REVERT: V 545 ASP cc_start: 0.6573 (t0) cc_final: 0.6124 (p0) REVERT: X 129 ARG cc_start: 0.5941 (tmt170) cc_final: 0.5255 (ttp-170) REVERT: X 331 ASP cc_start: 0.5511 (t0) cc_final: 0.5183 (p0) REVERT: X 566 MET cc_start: 0.6540 (tpt) cc_final: 0.6307 (tpt) REVERT: Z 117 MET cc_start: 0.4613 (mtm) cc_final: 0.4364 (mmm) REVERT: Z 129 ARG cc_start: 0.5966 (tmt170) cc_final: 0.5170 (ttp-170) REVERT: Z 259 MET cc_start: 0.3661 (mmp) cc_final: 0.3091 (mmt) REVERT: Z 444 TYR cc_start: 0.6322 (t80) cc_final: 0.5833 (t80) REVERT: Z 545 ASP cc_start: 0.6678 (t0) cc_final: 0.6090 (p0) REVERT: Z 628 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: Y 129 ARG cc_start: 0.5895 (tmt170) cc_final: 0.5204 (ttp-170) REVERT: Y 331 ASP cc_start: 0.5512 (t0) cc_final: 0.5181 (p0) REVERT: Y 566 MET cc_start: 0.6532 (tpt) cc_final: 0.6294 (tpt) outliers start: 69 outliers final: 7 residues processed: 969 average time/residue: 0.5547 time to fit residues: 865.0547 Evaluate side-chains 423 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 413 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 628 GLU Chi-restraints excluded: chain Y residue 363 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 572 optimal weight: 0.4980 chunk 513 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 531 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 395 optimal weight: 6.9990 chunk 615 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 236 GLN B 271 GLN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS B 634 ASN S 271 GLN ** S 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 634 ASN ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS V 236 GLN V 271 GLN ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 516 HIS V 634 ASN ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS X 236 GLN X 271 GLN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 634 ASN Z 271 GLN ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 634 ASN Y 13 ASN Y 212 HIS Y 271 GLN ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 634 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54480 Z= 0.200 Angle : 0.575 8.690 73716 Z= 0.302 Chirality : 0.046 0.144 8244 Planarity : 0.005 0.053 9630 Dihedral : 4.703 39.941 7682 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 1.77 % Allowed : 9.79 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 6852 helix: 0.40 (0.12), residues: 2142 sheet: -0.33 (0.17), residues: 1098 loop : -1.95 (0.10), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 396 HIS 0.006 0.001 HIS C 229 PHE 0.012 0.001 PHE G 76 TYR 0.014 0.001 TYR Z 86 ARG 0.004 0.000 ARG S 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 468 time to evaluate : 4.496 Fit side-chains REVERT: B 129 ARG cc_start: 0.5987 (tmt170) cc_final: 0.5172 (ttm170) REVERT: B 259 MET cc_start: 0.3494 (mmp) cc_final: 0.2870 (mmt) REVERT: C 249 MET cc_start: 0.8459 (mmt) cc_final: 0.8237 (mmt) REVERT: D 271 PRO cc_start: 0.7333 (Cg_endo) cc_final: 0.7105 (Cg_exo) REVERT: E 78 MET cc_start: 0.7912 (mmm) cc_final: 0.7354 (mmm) REVERT: E 197 MET cc_start: 0.8845 (mtp) cc_final: 0.8548 (mtp) REVERT: G 249 MET cc_start: 0.8456 (mmt) cc_final: 0.8231 (mmt) REVERT: H 78 MET cc_start: 0.7935 (mmm) cc_final: 0.7382 (mmm) REVERT: H 197 MET cc_start: 0.8847 (mtp) cc_final: 0.8551 (mtp) REVERT: S 129 ARG cc_start: 0.5982 (tmt170) cc_final: 0.5163 (ttm170) REVERT: S 218 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4810 (mm) REVERT: S 259 MET cc_start: 0.3665 (mmp) cc_final: 0.3069 (mmt) REVERT: S 455 LYS cc_start: 0.4606 (tptt) cc_final: 0.4161 (tptp) REVERT: S 465 LEU cc_start: 0.8567 (tp) cc_final: 0.8344 (tt) REVERT: V 129 ARG cc_start: 0.6037 (tmt170) cc_final: 0.5205 (ttm170) REVERT: V 259 MET cc_start: 0.3435 (mmp) cc_final: 0.2857 (mmt) REVERT: X 80 GLN cc_start: 0.4875 (pm20) cc_final: 0.4289 (mp10) REVERT: X 407 MET cc_start: 0.7445 (tpt) cc_final: 0.7225 (tpt) REVERT: X 413 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: Z 129 ARG cc_start: 0.5993 (tmt170) cc_final: 0.5388 (ttp-170) REVERT: Z 218 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4561 (mm) REVERT: Z 259 MET cc_start: 0.3695 (mmp) cc_final: 0.3055 (mmt) REVERT: Z 316 MET cc_start: 0.5434 (mmp) cc_final: 0.4969 (mmp) REVERT: Z 455 LYS cc_start: 0.4605 (tptt) cc_final: 0.4164 (tptp) REVERT: Y 413 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6726 (mt-10) outliers start: 101 outliers final: 45 residues processed: 544 average time/residue: 0.5380 time to fit residues: 481.9933 Evaluate side-chains 390 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 341 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 351 ASN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 413 GLU Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 662 VAL Chi-restraints excluded: chain Y residue 13 ASN Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 351 ASN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 413 GLU Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 342 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 512 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 616 optimal weight: 0.0970 chunk 666 optimal weight: 7.9990 chunk 549 optimal weight: 10.0000 chunk 611 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 494 optimal weight: 0.0270 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 103 ASN ** S 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 ASN ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 285 GLN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 13 ASN Y 212 HIS Y 236 GLN Y 285 GLN ** Y 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54480 Z= 0.219 Angle : 0.559 9.946 73716 Z= 0.293 Chirality : 0.046 0.220 8244 Planarity : 0.005 0.052 9630 Dihedral : 4.449 31.722 7658 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 2.17 % Allowed : 12.42 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.10), residues: 6852 helix: 0.23 (0.11), residues: 2190 sheet: -0.32 (0.17), residues: 1140 loop : -1.90 (0.10), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP V 396 HIS 0.019 0.001 HIS Y 212 PHE 0.011 0.001 PHE V 353 TYR 0.020 0.001 TYR X 272 ARG 0.004 0.000 ARG S 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 387 time to evaluate : 4.432 Fit side-chains revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5915 (tmt170) cc_final: 0.5048 (ttm170) REVERT: B 259 MET cc_start: 0.3759 (mmp) cc_final: 0.3100 (mmt) REVERT: B 617 MET cc_start: 0.5346 (OUTLIER) cc_final: 0.4954 (tpt) REVERT: D 50 MET cc_start: 0.8714 (tpp) cc_final: 0.8411 (tpt) REVERT: D 78 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6120 (tmm) REVERT: D 271 PRO cc_start: 0.7320 (Cg_endo) cc_final: 0.7086 (Cg_exo) REVERT: E 197 MET cc_start: 0.8878 (mtp) cc_final: 0.8659 (mtp) REVERT: E 291 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8377 (t) REVERT: F 50 MET cc_start: 0.8718 (tpp) cc_final: 0.8408 (tpt) REVERT: F 78 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6125 (tmm) REVERT: F 271 PRO cc_start: 0.7277 (Cg_endo) cc_final: 0.7057 (Cg_exo) REVERT: H 197 MET cc_start: 0.8874 (mtp) cc_final: 0.8621 (mtp) REVERT: S 77 THR cc_start: 0.3898 (OUTLIER) cc_final: 0.3439 (m) REVERT: S 129 ARG cc_start: 0.6085 (tmt170) cc_final: 0.5451 (ptt180) REVERT: S 238 ARG cc_start: 0.5176 (mmt90) cc_final: 0.4871 (mtm180) REVERT: S 259 MET cc_start: 0.3636 (mmp) cc_final: 0.3022 (mmt) REVERT: S 316 MET cc_start: 0.5438 (mmp) cc_final: 0.5086 (mmp) REVERT: S 455 LYS cc_start: 0.4804 (tptt) cc_final: 0.4373 (tptp) REVERT: V 129 ARG cc_start: 0.5896 (tmt170) cc_final: 0.5035 (ttm170) REVERT: V 259 MET cc_start: 0.3605 (mmp) cc_final: 0.2991 (mmt) REVERT: V 617 MET cc_start: 0.5355 (OUTLIER) cc_final: 0.4999 (tpt) REVERT: X 80 GLN cc_start: 0.4935 (pm20) cc_final: 0.4565 (mp10) REVERT: X 407 MET cc_start: 0.7549 (tpt) cc_final: 0.7125 (tpt) REVERT: X 413 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: Z 77 THR cc_start: 0.3975 (OUTLIER) cc_final: 0.3553 (m) REVERT: Z 129 ARG cc_start: 0.6094 (tmt170) cc_final: 0.5470 (ptt180) REVERT: Z 259 MET cc_start: 0.3735 (mmp) cc_final: 0.3051 (mmt) REVERT: Z 316 MET cc_start: 0.5522 (mmp) cc_final: 0.5188 (mmp) REVERT: Z 455 LYS cc_start: 0.4790 (tptt) cc_final: 0.4377 (tptp) REVERT: Y 413 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6797 (mt-10) outliers start: 124 outliers final: 80 residues processed: 484 average time/residue: 0.5249 time to fit residues: 423.9051 Evaluate side-chains 415 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 326 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 224 ASN Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 443 ASN Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 617 MET Chi-restraints excluded: chain V residue 628 GLU Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 413 GLU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 157 TYR Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 443 ASN Chi-restraints excluded: chain Z residue 465 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 662 VAL Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 413 GLU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 609 optimal weight: 20.0000 chunk 463 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 294 optimal weight: 0.7980 chunk 414 optimal weight: 10.0000 chunk 619 optimal weight: 8.9990 chunk 655 optimal weight: 0.7980 chunk 323 optimal weight: 6.9990 chunk 586 optimal weight: 9.9990 chunk 176 optimal weight: 0.0670 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 301 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 301 HIS ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 HIS ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 516 HIS Y 212 HIS Y 301 HIS ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54480 Z= 0.166 Angle : 0.514 10.014 73716 Z= 0.269 Chirality : 0.045 0.431 8244 Planarity : 0.004 0.050 9630 Dihedral : 4.183 31.855 7658 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.06 % Favored : 95.93 % Rotamer: Outliers : 2.33 % Allowed : 13.36 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 6852 helix: 0.26 (0.11), residues: 2202 sheet: 0.29 (0.17), residues: 1056 loop : -1.89 (0.09), residues: 3594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 396 HIS 0.004 0.001 HIS G 229 PHE 0.022 0.001 PHE X 288 TYR 0.016 0.001 TYR X 444 ARG 0.005 0.000 ARG V 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 383 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 ARG cc_start: 0.5687 (tmt170) cc_final: 0.4874 (ttm170) REVERT: B 212 HIS cc_start: 0.6310 (OUTLIER) cc_final: 0.6107 (t-170) REVERT: B 259 MET cc_start: 0.3582 (mmp) cc_final: 0.2981 (mmt) REVERT: B 617 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5070 (tpt) REVERT: C 70 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: G 70 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: S 77 THR cc_start: 0.3832 (OUTLIER) cc_final: 0.3339 (m) REVERT: S 129 ARG cc_start: 0.5879 (tmt170) cc_final: 0.5339 (ptt180) REVERT: S 259 MET cc_start: 0.3579 (mmp) cc_final: 0.2740 (mmt) REVERT: V 129 ARG cc_start: 0.5694 (tmt170) cc_final: 0.5335 (ptt180) REVERT: V 259 MET cc_start: 0.3526 (mmp) cc_final: 0.2960 (mmt) REVERT: V 442 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.4859 (m) REVERT: V 617 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.5077 (tpt) REVERT: X 80 GLN cc_start: 0.4890 (pm20) cc_final: 0.4658 (mp10) REVERT: X 201 MET cc_start: 0.1802 (OUTLIER) cc_final: 0.1438 (mmm) REVERT: X 413 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: Z 77 THR cc_start: 0.3844 (OUTLIER) cc_final: 0.3346 (m) REVERT: Z 129 ARG cc_start: 0.5820 (tmt170) cc_final: 0.5343 (ptt180) REVERT: Z 218 ILE cc_start: 0.4658 (OUTLIER) cc_final: 0.4359 (mm) REVERT: Z 259 MET cc_start: 0.3665 (mmp) cc_final: 0.2755 (mmt) REVERT: Y 91 GLU cc_start: 0.3904 (pm20) cc_final: 0.3584 (mt-10) REVERT: Y 201 MET cc_start: 0.1687 (OUTLIER) cc_final: 0.1334 (mmm) REVERT: Y 413 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6758 (mt-10) outliers start: 133 outliers final: 79 residues processed: 493 average time/residue: 0.5147 time to fit residues: 429.3199 Evaluate side-chains 407 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 315 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 212 HIS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 619 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 157 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 442 THR Chi-restraints excluded: chain V residue 617 MET Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 201 MET Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 363 GLN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 413 GLU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 443 ASN Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 363 GLN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 413 GLU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 545 optimal weight: 6.9990 chunk 372 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 487 optimal weight: 5.9990 chunk 270 optimal weight: 0.2980 chunk 559 optimal weight: 4.9990 chunk 453 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 334 optimal weight: 4.9990 chunk 588 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** D 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 516 HIS S 637 HIS ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 637 HIS ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 212 HIS ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 637 HIS ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 637 HIS Y 212 HIS ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 54480 Z= 0.293 Angle : 0.598 9.808 73716 Z= 0.316 Chirality : 0.047 0.302 8244 Planarity : 0.005 0.048 9630 Dihedral : 4.847 55.201 7658 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 3.17 % Allowed : 14.04 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 6852 helix: -0.03 (0.11), residues: 2190 sheet: -0.06 (0.17), residues: 1074 loop : -1.92 (0.09), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP V 396 HIS 0.021 0.002 HIS X 212 PHE 0.020 0.002 PHE Y 288 TYR 0.026 0.002 TYR Z 444 ARG 0.004 0.001 ARG G 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 335 time to evaluate : 4.505 Fit side-chains REVERT: B 259 MET cc_start: 0.3473 (mmp) cc_final: 0.2883 (mmt) REVERT: B 363 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6862 (pt0) REVERT: B 382 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6813 (mt) REVERT: B 530 MET cc_start: 0.7386 (ptp) cc_final: 0.7172 (ttp) REVERT: C 70 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: G 70 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: S 129 ARG cc_start: 0.5998 (tmt170) cc_final: 0.5345 (ttp-170) REVERT: S 259 MET cc_start: 0.3492 (mmp) cc_final: 0.2800 (mmt) REVERT: S 455 LYS cc_start: 0.5325 (tptt) cc_final: 0.4529 (tptp) REVERT: V 259 MET cc_start: 0.3532 (mmp) cc_final: 0.2901 (mmt) REVERT: V 363 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6890 (pt0) REVERT: V 382 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6811 (mt) REVERT: V 530 MET cc_start: 0.7386 (ptp) cc_final: 0.7173 (ttp) REVERT: X 80 GLN cc_start: 0.4658 (pm20) cc_final: 0.4446 (mp10) REVERT: X 91 GLU cc_start: 0.3743 (pm20) cc_final: 0.3294 (mt-10) REVERT: X 201 MET cc_start: 0.2022 (OUTLIER) cc_final: 0.1773 (mmm) REVERT: X 382 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.6977 (mt) REVERT: X 413 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7005 (mt-10) REVERT: X 617 MET cc_start: 0.5958 (OUTLIER) cc_final: 0.5398 (tpp) REVERT: Z 77 THR cc_start: 0.3872 (OUTLIER) cc_final: 0.3589 (t) REVERT: Z 129 ARG cc_start: 0.5981 (tmt170) cc_final: 0.5453 (ptt180) REVERT: Z 218 ILE cc_start: 0.4786 (OUTLIER) cc_final: 0.4435 (mm) REVERT: Z 259 MET cc_start: 0.3617 (mmp) cc_final: 0.2858 (mmt) REVERT: Z 455 LYS cc_start: 0.5163 (tptt) cc_final: 0.4329 (tptp) REVERT: Y 91 GLU cc_start: 0.4150 (pm20) cc_final: 0.3522 (mt-10) REVERT: Y 201 MET cc_start: 0.1945 (OUTLIER) cc_final: 0.1724 (mmm) REVERT: Y 382 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6954 (mt) REVERT: Y 413 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: Y 617 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.5494 (tpp) outliers start: 181 outliers final: 109 residues processed: 485 average time/residue: 0.4945 time to fit residues: 408.0652 Evaluate side-chains 435 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 310 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 375 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 201 MET Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 201 MET Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 413 GLU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 617 MET Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 443 ASN Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 413 GLU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 617 MET Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 220 optimal weight: 0.7980 chunk 590 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 384 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 655 optimal weight: 6.9990 chunk 544 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 212 HIS ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 501 GLN ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 516 HIS Y 637 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 54480 Z= 0.238 Angle : 0.554 11.257 73716 Z= 0.292 Chirality : 0.046 0.327 8244 Planarity : 0.005 0.057 9630 Dihedral : 4.739 51.290 7658 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 3.46 % Allowed : 14.36 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.10), residues: 6852 helix: -0.06 (0.11), residues: 2184 sheet: 0.07 (0.17), residues: 1044 loop : -1.89 (0.09), residues: 3624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 396 HIS 0.021 0.001 HIS X 212 PHE 0.014 0.001 PHE Y 288 TYR 0.018 0.001 TYR Z 444 ARG 0.004 0.000 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 319 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 MET cc_start: 0.3424 (mmp) cc_final: 0.2875 (mmt) REVERT: B 382 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6947 (mt) REVERT: B 530 MET cc_start: 0.7345 (ptp) cc_final: 0.7121 (ttp) REVERT: C 70 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: G 70 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: S 129 ARG cc_start: 0.5891 (tmt170) cc_final: 0.5382 (ptt180) REVERT: S 259 MET cc_start: 0.3446 (mmp) cc_final: 0.2770 (mmt) REVERT: S 382 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7166 (mt) REVERT: S 455 LYS cc_start: 0.5262 (tptt) cc_final: 0.4660 (tptp) REVERT: V 259 MET cc_start: 0.3577 (mmp) cc_final: 0.2973 (mmt) REVERT: V 382 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6949 (mt) REVERT: V 530 MET cc_start: 0.7346 (ptp) cc_final: 0.7118 (ttp) REVERT: X 201 MET cc_start: 0.1555 (OUTLIER) cc_final: 0.1355 (mmm) REVERT: Z 77 THR cc_start: 0.3778 (OUTLIER) cc_final: 0.3437 (t) REVERT: Z 129 ARG cc_start: 0.5894 (tmt170) cc_final: 0.5387 (ptt180) REVERT: Z 218 ILE cc_start: 0.4777 (OUTLIER) cc_final: 0.4338 (mm) REVERT: Z 259 MET cc_start: 0.3660 (mmp) cc_final: 0.3054 (mmt) REVERT: Z 382 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7174 (mt) REVERT: Z 455 LYS cc_start: 0.5264 (tptt) cc_final: 0.4663 (tptp) REVERT: Y 91 GLU cc_start: 0.4124 (pm20) cc_final: 0.3461 (mt-10) REVERT: Y 201 MET cc_start: 0.1674 (OUTLIER) cc_final: 0.1422 (mmm) outliers start: 198 outliers final: 125 residues processed: 484 average time/residue: 0.4898 time to fit residues: 405.9145 Evaluate side-chains 432 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 297 time to evaluate : 5.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 157 TYR Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 157 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 443 ASN Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 201 MET Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 443 ASN Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 201 MET Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 632 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 373 optimal weight: 9.9990 chunk 479 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 552 optimal weight: 4.9990 chunk 366 optimal weight: 20.0000 chunk 653 optimal weight: 9.9990 chunk 408 optimal weight: 9.9990 chunk 398 optimal weight: 0.9980 chunk 301 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN D 42 HIS F 42 HIS G 164 ASN ** S 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 639 GLN ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 54480 Z= 0.346 Angle : 0.630 10.925 73716 Z= 0.334 Chirality : 0.049 0.311 8244 Planarity : 0.005 0.055 9630 Dihedral : 5.303 57.479 7658 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.39 % Favored : 93.59 % Rotamer: Outliers : 3.29 % Allowed : 14.95 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 6852 helix: -0.33 (0.11), residues: 2190 sheet: -0.47 (0.16), residues: 1098 loop : -1.92 (0.09), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 514 HIS 0.007 0.001 HIS E 229 PHE 0.013 0.002 PHE X 95 TYR 0.023 0.002 TYR Z 414 ARG 0.005 0.001 ARG V 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 309 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 MET cc_start: 0.3443 (mmp) cc_final: 0.2899 (mmt) REVERT: C 70 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: D 50 MET cc_start: 0.8484 (tpt) cc_final: 0.8167 (tpt) REVERT: F 50 MET cc_start: 0.8479 (tpt) cc_final: 0.8159 (tpt) REVERT: G 70 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: S 129 ARG cc_start: 0.6054 (tmt170) cc_final: 0.5396 (ttp-170) REVERT: S 259 MET cc_start: 0.3462 (mmp) cc_final: 0.2775 (mmt) REVERT: S 378 GLU cc_start: 0.6919 (tp30) cc_final: 0.6552 (tp30) REVERT: S 382 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7172 (mt) REVERT: S 455 LYS cc_start: 0.5397 (tptt) cc_final: 0.4565 (tptp) REVERT: S 530 MET cc_start: 0.7141 (ptp) cc_final: 0.6695 (ptp) REVERT: V 259 MET cc_start: 0.3587 (mmp) cc_final: 0.3040 (mmt) REVERT: V 440 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.4994 (tp) REVERT: X 382 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6857 (mt) REVERT: Z 129 ARG cc_start: 0.5973 (tmt170) cc_final: 0.5116 (ttm170) REVERT: Z 218 ILE cc_start: 0.4928 (OUTLIER) cc_final: 0.4473 (mm) REVERT: Z 259 MET cc_start: 0.3629 (mmp) cc_final: 0.3017 (mmt) REVERT: Z 382 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7177 (mt) REVERT: Z 455 LYS cc_start: 0.5419 (tptt) cc_final: 0.4591 (tptp) REVERT: Y 382 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6796 (mt) outliers start: 188 outliers final: 140 residues processed: 458 average time/residue: 0.5005 time to fit residues: 390.8441 Evaluate side-chains 444 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 296 time to evaluate : 4.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 157 TYR Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 399 ASP Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain S residue 639 GLN Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 TYR Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 172 MET Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 278 VAL Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 295 THR Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 382 ILE Chi-restraints excluded: chain V residue 389 LEU Chi-restraints excluded: chain V residue 440 ILE Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 619 VAL Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 277 THR Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 288 PHE Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 351 ASN Chi-restraints excluded: chain X residue 366 THR Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 619 VAL Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 399 ASP Chi-restraints excluded: chain Z residue 465 LEU Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 277 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 351 ASN Chi-restraints excluded: chain Y residue 366 THR Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 619 VAL Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 404 optimal weight: 9.9990 chunk 260 optimal weight: 0.4980 chunk 390 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 415 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 chunk 323 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 513 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN E 164 ASN F 164 ASN H 164 ASN ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 315 GLN ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 516 HIS ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 639 GLN Y 280 ASN ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 54480 Z= 0.164 Angle : 0.528 11.863 73716 Z= 0.275 Chirality : 0.045 0.295 8244 Planarity : 0.004 0.054 9630 Dihedral : 4.611 55.029 7658 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.75 % Allowed : 15.88 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.10), residues: 6852 helix: -0.09 (0.11), residues: 2232 sheet: -0.29 (0.17), residues: 1032 loop : -1.76 (0.09), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 396 HIS 0.003 0.001 HIS G 229 PHE 0.009 0.001 PHE X 95 TYR 0.024 0.001 TYR S 444 ARG 0.006 0.000 ARG V 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 322 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 259 MET cc_start: 0.3495 (mmp) cc_final: 0.2924 (mmt) REVERT: B 378 GLU cc_start: 0.6562 (tp30) cc_final: 0.6298 (tp30) REVERT: C 70 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: G 70 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: S 129 ARG cc_start: 0.5947 (tmt170) cc_final: 0.4938 (tpp80) REVERT: S 135 ILE cc_start: 0.4731 (OUTLIER) cc_final: 0.4306 (mt) REVERT: S 218 ILE cc_start: 0.4910 (OUTLIER) cc_final: 0.4451 (mm) REVERT: S 259 MET cc_start: 0.3439 (mmp) cc_final: 0.2715 (mmt) REVERT: S 378 GLU cc_start: 0.6732 (tp30) cc_final: 0.6408 (tp30) REVERT: S 382 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7091 (mt) REVERT: S 455 LYS cc_start: 0.5211 (tptt) cc_final: 0.4367 (tptp) REVERT: V 259 MET cc_start: 0.3499 (mmp) cc_final: 0.2938 (mmt) REVERT: V 378 GLU cc_start: 0.6558 (tp30) cc_final: 0.6296 (tp30) REVERT: X 26 ARG cc_start: 0.6164 (mmm160) cc_final: 0.5723 (mmp80) REVERT: X 172 MET cc_start: 0.3199 (tpt) cc_final: 0.2237 (tmm) REVERT: X 382 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7094 (pt) REVERT: Z 129 ARG cc_start: 0.5943 (tmt170) cc_final: 0.5149 (ttm170) REVERT: Z 218 ILE cc_start: 0.4846 (OUTLIER) cc_final: 0.4303 (mm) REVERT: Z 259 MET cc_start: 0.3446 (mmp) cc_final: 0.2849 (mmt) REVERT: Z 378 GLU cc_start: 0.6818 (tp30) cc_final: 0.6506 (tp30) REVERT: Z 382 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7085 (mt) REVERT: Z 455 LYS cc_start: 0.5211 (tptt) cc_final: 0.4364 (tptp) REVERT: Y 26 ARG cc_start: 0.6166 (mmm160) cc_final: 0.5728 (mmp80) REVERT: Y 172 MET cc_start: 0.3355 (tpt) cc_final: 0.2301 (tmm) REVERT: Y 382 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6968 (mt) outliers start: 157 outliers final: 124 residues processed: 448 average time/residue: 0.5184 time to fit residues: 390.5717 Evaluate side-chains 433 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 300 time to evaluate : 4.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 157 TYR Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 382 ILE Chi-restraints excluded: chain S residue 399 ASP Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 619 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 157 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 443 ASN Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 363 GLN Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 382 ILE Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 550 THR Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Z residue 639 GLN Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 594 optimal weight: 1.9990 chunk 626 optimal weight: 0.4980 chunk 571 optimal weight: 8.9990 chunk 608 optimal weight: 20.0000 chunk 625 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 478 optimal weight: 0.0010 chunk 186 optimal weight: 0.9990 chunk 550 optimal weight: 5.9990 chunk 575 optimal weight: 9.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 54480 Z= 0.163 Angle : 0.519 11.716 73716 Z= 0.270 Chirality : 0.045 0.276 8244 Planarity : 0.004 0.055 9630 Dihedral : 4.485 55.396 7658 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.54 % Allowed : 16.00 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 6852 helix: 0.05 (0.11), residues: 2226 sheet: -0.20 (0.17), residues: 1038 loop : -1.70 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 396 HIS 0.006 0.001 HIS Z 637 PHE 0.009 0.001 PHE X 95 TYR 0.023 0.001 TYR V 444 ARG 0.007 0.000 ARG Z 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 318 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 259 MET cc_start: 0.3387 (mmp) cc_final: 0.2820 (mmt) REVERT: B 378 GLU cc_start: 0.6575 (tp30) cc_final: 0.6375 (tp30) REVERT: B 654 THR cc_start: 0.5284 (OUTLIER) cc_final: 0.5069 (p) REVERT: C 70 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: G 70 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: S 129 ARG cc_start: 0.5899 (tmt170) cc_final: 0.5216 (ttm170) REVERT: S 135 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4588 (mt) REVERT: S 259 MET cc_start: 0.3452 (mmp) cc_final: 0.2702 (mmt) REVERT: S 378 GLU cc_start: 0.6693 (tp30) cc_final: 0.6376 (tp30) REVERT: S 455 LYS cc_start: 0.5109 (tptt) cc_final: 0.4293 (tptp) REVERT: V 259 MET cc_start: 0.3414 (mmp) cc_final: 0.2849 (mmt) REVERT: V 654 THR cc_start: 0.5301 (OUTLIER) cc_final: 0.5082 (p) REVERT: X 26 ARG cc_start: 0.6061 (mmm160) cc_final: 0.5645 (mmp80) REVERT: X 172 MET cc_start: 0.3237 (tpt) cc_final: 0.2289 (tmm) REVERT: Z 129 ARG cc_start: 0.5940 (tmt170) cc_final: 0.5108 (ttm170) REVERT: Z 218 ILE cc_start: 0.4897 (OUTLIER) cc_final: 0.4267 (mm) REVERT: Z 259 MET cc_start: 0.3597 (mmp) cc_final: 0.2896 (mmt) REVERT: Z 378 GLU cc_start: 0.6691 (tp30) cc_final: 0.6371 (tp30) REVERT: Z 455 LYS cc_start: 0.5108 (tptt) cc_final: 0.4259 (tptp) REVERT: Y 26 ARG cc_start: 0.6057 (mmm160) cc_final: 0.5639 (mmp80) REVERT: Y 172 MET cc_start: 0.3188 (tpt) cc_final: 0.2196 (tmm) REVERT: Y 382 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7063 (pt) outliers start: 145 outliers final: 124 residues processed: 437 average time/residue: 0.5546 time to fit residues: 411.7203 Evaluate side-chains 434 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 303 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 157 TYR Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 363 GLN Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 399 ASP Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 157 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 363 GLN Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain V residue 654 THR Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 361 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 419 LEU Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 218 ILE Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 288 PHE Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 419 LEU Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 606 optimal weight: 0.7980 chunk 399 optimal weight: 10.0000 chunk 643 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 305 optimal weight: 0.0050 chunk 447 optimal weight: 6.9990 chunk 675 optimal weight: 5.9990 chunk 621 optimal weight: 0.8980 chunk 537 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 415 optimal weight: 3.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 315 GLN ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 315 GLN ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54480 Z= 0.225 Angle : 0.552 11.246 73716 Z= 0.289 Chirality : 0.046 0.253 8244 Planarity : 0.005 0.053 9630 Dihedral : 4.737 55.924 7658 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.48 % Allowed : 16.07 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.10), residues: 6852 helix: -0.03 (0.11), residues: 2202 sheet: -0.26 (0.17), residues: 1014 loop : -1.73 (0.09), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 396 HIS 0.004 0.001 HIS D 229 PHE 0.011 0.001 PHE X 290 TYR 0.019 0.001 TYR X 86 ARG 0.007 0.000 ARG V 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 303 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 259 MET cc_start: 0.3397 (mmp) cc_final: 0.2836 (mmt) REVERT: B 378 GLU cc_start: 0.6689 (tp30) cc_final: 0.6455 (tp30) REVERT: C 70 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: G 70 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: S 135 ILE cc_start: 0.4998 (OUTLIER) cc_final: 0.4649 (mt) REVERT: S 218 ILE cc_start: 0.4916 (OUTLIER) cc_final: 0.4460 (mm) REVERT: S 259 MET cc_start: 0.3444 (mmp) cc_final: 0.2690 (mmt) REVERT: S 455 LYS cc_start: 0.5167 (tptt) cc_final: 0.4345 (tptp) REVERT: V 259 MET cc_start: 0.3575 (mmp) cc_final: 0.2994 (mmt) REVERT: V 654 THR cc_start: 0.5365 (OUTLIER) cc_final: 0.5163 (p) REVERT: X 26 ARG cc_start: 0.6212 (mmm160) cc_final: 0.5791 (mmp80) REVERT: X 172 MET cc_start: 0.3242 (tpt) cc_final: 0.2219 (tmm) REVERT: Z 129 ARG cc_start: 0.6020 (tmt170) cc_final: 0.4912 (tpp80) REVERT: Z 259 MET cc_start: 0.3596 (mmp) cc_final: 0.2903 (mmt) REVERT: Z 378 GLU cc_start: 0.6754 (tp30) cc_final: 0.6406 (tp30) REVERT: Z 455 LYS cc_start: 0.5158 (tptt) cc_final: 0.4336 (tptp) REVERT: Y 26 ARG cc_start: 0.6204 (mmm160) cc_final: 0.5785 (mmp80) REVERT: Y 172 MET cc_start: 0.3148 (tpt) cc_final: 0.2094 (tmm) REVERT: Y 358 ARG cc_start: 0.5736 (tpp80) cc_final: 0.5528 (tpp80) outliers start: 142 outliers final: 125 residues processed: 414 average time/residue: 0.5085 time to fit residues: 356.3237 Evaluate side-chains 429 residues out of total 5718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 299 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 70 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 522 LEU Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 371 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 135 ILE Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain S residue 218 ILE Chi-restraints excluded: chain S residue 277 THR Chi-restraints excluded: chain S residue 278 VAL Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 366 THR Chi-restraints excluded: chain S residue 399 ASP Chi-restraints excluded: chain S residue 443 ASN Chi-restraints excluded: chain S residue 509 VAL Chi-restraints excluded: chain S residue 550 THR Chi-restraints excluded: chain S residue 619 VAL Chi-restraints excluded: chain S residue 636 ILE Chi-restraints excluded: chain V residue 16 GLU Chi-restraints excluded: chain V residue 77 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 155 ILE Chi-restraints excluded: chain V residue 157 TYR Chi-restraints excluded: chain V residue 203 VAL Chi-restraints excluded: chain V residue 218 ILE Chi-restraints excluded: chain V residue 277 THR Chi-restraints excluded: chain V residue 293 MET Chi-restraints excluded: chain V residue 303 ILE Chi-restraints excluded: chain V residue 325 LEU Chi-restraints excluded: chain V residue 509 VAL Chi-restraints excluded: chain V residue 550 THR Chi-restraints excluded: chain V residue 576 MET Chi-restraints excluded: chain V residue 636 ILE Chi-restraints excluded: chain V residue 654 THR Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 133 THR Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain X residue 203 VAL Chi-restraints excluded: chain X residue 212 HIS Chi-restraints excluded: chain X residue 218 ILE Chi-restraints excluded: chain X residue 278 VAL Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 325 LEU Chi-restraints excluded: chain X residue 361 MET Chi-restraints excluded: chain X residue 382 ILE Chi-restraints excluded: chain X residue 443 ASN Chi-restraints excluded: chain X residue 550 THR Chi-restraints excluded: chain X residue 636 ILE Chi-restraints excluded: chain X residue 662 VAL Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 132 VAL Chi-restraints excluded: chain Z residue 155 ILE Chi-restraints excluded: chain Z residue 203 VAL Chi-restraints excluded: chain Z residue 212 HIS Chi-restraints excluded: chain Z residue 277 THR Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain Z residue 366 THR Chi-restraints excluded: chain Z residue 509 VAL Chi-restraints excluded: chain Z residue 530 MET Chi-restraints excluded: chain Z residue 619 VAL Chi-restraints excluded: chain Z residue 636 ILE Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 77 THR Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 203 VAL Chi-restraints excluded: chain Y residue 212 HIS Chi-restraints excluded: chain Y residue 218 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 325 LEU Chi-restraints excluded: chain Y residue 382 ILE Chi-restraints excluded: chain Y residue 443 ASN Chi-restraints excluded: chain Y residue 550 THR Chi-restraints excluded: chain Y residue 636 ILE Chi-restraints excluded: chain Y residue 662 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 329 optimal weight: 4.9990 chunk 427 optimal weight: 0.1980 chunk 572 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 495 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 538 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 553 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 301 HIS X 301 HIS ** X 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118470 restraints weight = 98662.966| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.96 r_work: 0.3383 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54480 Z= 0.131 Angle : 0.496 11.426 73716 Z= 0.256 Chirality : 0.044 0.257 8244 Planarity : 0.004 0.057 9630 Dihedral : 4.189 55.660 7658 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.05 % Allowed : 16.53 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.10), residues: 6852 helix: 0.17 (0.11), residues: 2238 sheet: 0.07 (0.18), residues: 996 loop : -1.59 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 396 HIS 0.002 0.000 HIS C 105 PHE 0.008 0.001 PHE X 290 TYR 0.022 0.001 TYR V 444 ARG 0.007 0.000 ARG B 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9455.66 seconds wall clock time: 168 minutes 24.49 seconds (10104.49 seconds total)