Starting phenix.real_space_refine on Tue Sep 24 17:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xc2_33112/09_2024/7xc2_33112.cif" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 240 5.16 5 C 33300 2.51 5 N 8745 2.21 5 O 9770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 52070 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 6852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6852 Classifications: {'peptide': 858} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3531 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.75, per 1000 atoms: 0.42 Number of scatterers: 52070 At special positions: 0 Unit cell: (249.7, 246.4, 110, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 240 16.00 P 15 15.00 O 9770 8.00 N 8745 7.00 C 33300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.01 Conformation dependent library (CDL) restraints added in 5.1 seconds 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12310 Finding SS restraints... Secondary structure from input PDB file: 305 helices and 30 sheets defined 57.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'C' and resid 22 through 51 Processing helix chain 'C' and resid 59 through 87 Processing helix chain 'C' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.731A pdb=" N GLU C 167 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.562A pdb=" N HIS C 191 " --> pdb=" O TRP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 234 through 247 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.507A pdb=" N LEU C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 4.330A pdb=" N TRP C 290 " --> pdb=" O ASN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 298 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.595A pdb=" N SER C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 356 through 368 Processing helix chain 'C' and resid 370 through 383 removed outlier: 3.594A pdb=" N ASN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'C' and resid 418 through 423 Processing helix chain 'C' and resid 425 through 427 No H-bonds generated for 'chain 'C' and resid 425 through 427' Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 435 through 438 removed outlier: 3.648A pdb=" N PHE C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 446 through 457 Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 502 through 515 Processing helix chain 'C' and resid 566 through 570 Processing helix chain 'C' and resid 617 through 621 Processing helix chain 'C' and resid 638 through 644 Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 680 through 687 removed outlier: 3.760A pdb=" N VAL C 684 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 690 No H-bonds generated for 'chain 'C' and resid 688 through 690' Processing helix chain 'C' and resid 707 through 717 removed outlier: 3.515A pdb=" N LEU C 711 " --> pdb=" O MET C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.863A pdb=" N ILE C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN C 766 " --> pdb=" O SER C 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 766' Processing helix chain 'C' and resid 787 through 793 Processing helix chain 'C' and resid 805 through 809 Processing helix chain 'C' and resid 862 through 865 removed outlier: 4.368A pdb=" N SER C 865 " --> pdb=" O LYS C 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 862 through 865' Processing helix chain 'C' and resid 892 through 910 removed outlier: 3.661A pdb=" N GLU C 898 " --> pdb=" O GLU C 894 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.736A pdb=" N ASP D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 removed outlier: 4.206A pdb=" N GLN D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 174 through 203 removed outlier: 4.323A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.839A pdb=" N LEU D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 245 Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.826A pdb=" N SER D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 289 Processing helix chain 'D' and resid 290 through 316 removed outlier: 3.855A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.533A pdb=" N MET D 327 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP D 328 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 329 " --> pdb=" O MET D 326 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 330 " --> pdb=" O MET D 327 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP D 331 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN D 332 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.739A pdb=" N LYS D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 365 removed outlier: 3.536A pdb=" N GLY D 360 " --> pdb=" O TRP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 4.105A pdb=" N TYR D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 397 Processing helix chain 'D' and resid 400 through 418 Processing helix chain 'D' and resid 423 through 441 removed outlier: 3.559A pdb=" N ARG D 427 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 455 removed outlier: 3.565A pdb=" N ASP D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 452 " --> pdb=" O PHE D 448 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS D 453 " --> pdb=" O THR D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 481 removed outlier: 3.822A pdb=" N GLU D 481 " --> pdb=" O HIS D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'D' and resid 510 through 530 removed outlier: 4.206A pdb=" N VAL D 516 " --> pdb=" O LYS D 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 561 removed outlier: 3.690A pdb=" N GLN D 538 " --> pdb=" O ASN D 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU D 539 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D 540 " --> pdb=" O ILE D 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP D 542 " --> pdb=" O GLN D 538 " (cutoff:3.500A) Proline residue: D 543 - end of helix Proline residue: D 556 - end of helix removed outlier: 3.639A pdb=" N LEU D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 51 Processing helix chain 'A' and resid 59 through 87 Processing helix chain 'A' and resid 114 through 141 removed outlier: 3.858A pdb=" N TYR A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.732A pdb=" N GLU A 167 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.562A pdb=" N HIS A 191 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 234 through 247 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.506A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 4.331A pdb=" N TRP A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 298 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.595A pdb=" N SER A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.594A pdb=" N ASN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 435 through 438 removed outlier: 3.648A pdb=" N PHE A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 502 through 515 Processing helix chain 'A' and resid 566 through 570 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 638 through 644 Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.761A pdb=" N VAL A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 707 through 717 removed outlier: 3.513A pdb=" N LEU A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.863A pdb=" N ILE A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN A 766 " --> pdb=" O SER A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 766' Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 862 through 865 removed outlier: 4.369A pdb=" N SER A 865 " --> pdb=" O LYS A 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 862 through 865' Processing helix chain 'A' and resid 892 through 910 removed outlier: 3.661A pdb=" N GLU A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS A 910 " --> pdb=" O ALA A 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.736A pdb=" N ASP B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.206A pdb=" N GLN B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 174 through 203 removed outlier: 4.324A pdb=" N ALA B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 3.840A pdb=" N LEU B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 245 Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.826A pdb=" N SER B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 290 through 316 removed outlier: 3.855A pdb=" N ALA B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.533A pdb=" N MET B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 329 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 330 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TRP B 331 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLN B 332 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 removed outlier: 3.739A pdb=" N LYS B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.536A pdb=" N GLY B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 4.105A pdb=" N TYR B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 400 through 418 Processing helix chain 'B' and resid 423 through 441 removed outlier: 3.559A pdb=" N ARG B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.564A pdb=" N ASP B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 452 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 481 removed outlier: 3.822A pdb=" N GLU B 481 " --> pdb=" O HIS B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 510 through 530 removed outlier: 4.206A pdb=" N VAL B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 561 removed outlier: 3.690A pdb=" N GLN B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 540 " --> pdb=" O ILE B 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Proline residue: B 543 - end of helix Proline residue: B 556 - end of helix removed outlier: 3.639A pdb=" N LEU B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 51 Processing helix chain 'E' and resid 59 through 87 Processing helix chain 'E' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.732A pdb=" N GLU E 167 " --> pdb=" O ASP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 183 Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.562A pdb=" N HIS E 191 " --> pdb=" O TRP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 218 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 234 through 247 Processing helix chain 'E' and resid 253 through 257 Processing helix chain 'E' and resid 260 through 272 removed outlier: 3.505A pdb=" N LEU E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.330A pdb=" N TRP E 290 " --> pdb=" O ASN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 298 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.595A pdb=" N SER E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 346 Processing helix chain 'E' and resid 353 through 355 No H-bonds generated for 'chain 'E' and resid 353 through 355' Processing helix chain 'E' and resid 356 through 368 Processing helix chain 'E' and resid 370 through 383 removed outlier: 3.595A pdb=" N ASN E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 399 Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'E' and resid 418 through 423 Processing helix chain 'E' and resid 425 through 427 No H-bonds generated for 'chain 'E' and resid 425 through 427' Processing helix chain 'E' and resid 428 through 434 Processing helix chain 'E' and resid 435 through 438 removed outlier: 3.648A pdb=" N PHE E 438 " --> pdb=" O LEU E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 438' Processing helix chain 'E' and resid 446 through 457 Processing helix chain 'E' and resid 467 through 482 Processing helix chain 'E' and resid 502 through 515 Processing helix chain 'E' and resid 566 through 570 Processing helix chain 'E' and resid 617 through 621 Processing helix chain 'E' and resid 638 through 644 Processing helix chain 'E' and resid 661 through 665 Processing helix chain 'E' and resid 680 through 687 removed outlier: 3.761A pdb=" N VAL E 684 " --> pdb=" O ASP E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 707 through 717 removed outlier: 3.514A pdb=" N LEU E 711 " --> pdb=" O MET E 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 766 removed outlier: 3.863A pdb=" N ILE E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN E 766 " --> pdb=" O SER E 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 762 through 766' Processing helix chain 'E' and resid 787 through 793 Processing helix chain 'E' and resid 805 through 809 Processing helix chain 'E' and resid 862 through 865 removed outlier: 4.368A pdb=" N SER E 865 " --> pdb=" O LYS E 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 862 through 865' Processing helix chain 'E' and resid 892 through 910 removed outlier: 3.661A pdb=" N GLU E 898 " --> pdb=" O GLU E 894 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS E 910 " --> pdb=" O ALA E 906 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 removed outlier: 3.736A pdb=" N ASP F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 158 removed outlier: 4.207A pdb=" N GLN F 157 " --> pdb=" O PHE F 153 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 165 Processing helix chain 'F' and resid 174 through 203 removed outlier: 4.323A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.839A pdb=" N LEU F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 245 Processing helix chain 'F' and resid 252 through 276 removed outlier: 3.825A pdb=" N SER F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 289 Processing helix chain 'F' and resid 290 through 316 removed outlier: 3.855A pdb=" N ALA F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS F 299 " --> pdb=" O LYS F 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 332 removed outlier: 3.532A pdb=" N MET F 327 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP F 328 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 329 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP F 330 " --> pdb=" O MET F 327 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP F 331 " --> pdb=" O ASP F 328 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN F 332 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 347 removed outlier: 3.739A pdb=" N LYS F 337 " --> pdb=" O PHE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 365 removed outlier: 3.536A pdb=" N GLY F 360 " --> pdb=" O TRP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 392 removed outlier: 4.105A pdb=" N TYR F 383 " --> pdb=" O ASP F 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA F 384 " --> pdb=" O GLY F 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 385 " --> pdb=" O ARG F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 397 Processing helix chain 'F' and resid 400 through 418 Processing helix chain 'F' and resid 423 through 441 removed outlier: 3.559A pdb=" N ARG F 427 " --> pdb=" O LEU F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 455 removed outlier: 3.565A pdb=" N ASP F 451 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU F 452 " --> pdb=" O PHE F 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS F 453 " --> pdb=" O THR F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 481 removed outlier: 3.822A pdb=" N GLU F 481 " --> pdb=" O HIS F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 484 No H-bonds generated for 'chain 'F' and resid 482 through 484' Processing helix chain 'F' and resid 510 through 530 removed outlier: 4.206A pdb=" N VAL F 516 " --> pdb=" O LYS F 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 561 removed outlier: 3.690A pdb=" N GLN F 538 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU F 539 " --> pdb=" O SER F 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS F 540 " --> pdb=" O ILE F 536 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP F 542 " --> pdb=" O GLN F 538 " (cutoff:3.500A) Proline residue: F 543 - end of helix Proline residue: F 556 - end of helix removed outlier: 3.638A pdb=" N LEU F 561 " --> pdb=" O VAL F 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 51 Processing helix chain 'G' and resid 59 through 87 Processing helix chain 'G' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR G 141 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 163 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.732A pdb=" N GLU G 167 " --> pdb=" O ASP G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.562A pdb=" N HIS G 191 " --> pdb=" O TRP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 218 Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 234 through 247 Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 260 through 272 removed outlier: 3.506A pdb=" N LEU G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 294 removed outlier: 4.331A pdb=" N TRP G 290 " --> pdb=" O ASN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 298 Processing helix chain 'G' and resid 312 through 320 removed outlier: 3.595A pdb=" N SER G 316 " --> pdb=" O ASN G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 346 Processing helix chain 'G' and resid 353 through 355 No H-bonds generated for 'chain 'G' and resid 353 through 355' Processing helix chain 'G' and resid 356 through 368 Processing helix chain 'G' and resid 370 through 383 removed outlier: 3.595A pdb=" N ASN G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 399 Processing helix chain 'G' and resid 408 through 418 Processing helix chain 'G' and resid 418 through 423 Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 428 through 434 Processing helix chain 'G' and resid 435 through 438 removed outlier: 3.648A pdb=" N PHE G 438 " --> pdb=" O LEU G 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 435 through 438' Processing helix chain 'G' and resid 446 through 457 Processing helix chain 'G' and resid 467 through 482 Processing helix chain 'G' and resid 502 through 515 Processing helix chain 'G' and resid 566 through 570 Processing helix chain 'G' and resid 617 through 621 Processing helix chain 'G' and resid 638 through 644 Processing helix chain 'G' and resid 661 through 665 Processing helix chain 'G' and resid 680 through 687 removed outlier: 3.760A pdb=" N VAL G 684 " --> pdb=" O ASP G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 690 No H-bonds generated for 'chain 'G' and resid 688 through 690' Processing helix chain 'G' and resid 707 through 717 removed outlier: 3.514A pdb=" N LEU G 711 " --> pdb=" O MET G 707 " (cutoff:3.500A) Processing helix chain 'G' and resid 762 through 766 removed outlier: 3.863A pdb=" N ILE G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN G 766 " --> pdb=" O SER G 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 762 through 766' Processing helix chain 'G' and resid 787 through 793 Processing helix chain 'G' and resid 805 through 809 Processing helix chain 'G' and resid 862 through 865 removed outlier: 4.369A pdb=" N SER G 865 " --> pdb=" O LYS G 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 862 through 865' Processing helix chain 'G' and resid 892 through 910 removed outlier: 3.662A pdb=" N GLU G 898 " --> pdb=" O GLU G 894 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS G 910 " --> pdb=" O ALA G 906 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 152 removed outlier: 3.736A pdb=" N ASP H 144 " --> pdb=" O SER H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 158 removed outlier: 4.206A pdb=" N GLN H 157 " --> pdb=" O PHE H 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN H 158 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'H' and resid 174 through 203 removed outlier: 4.323A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU H 199 " --> pdb=" O ASP H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 226 removed outlier: 3.839A pdb=" N LEU H 213 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 245 Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.826A pdb=" N SER H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 289 Processing helix chain 'H' and resid 290 through 316 removed outlier: 3.854A pdb=" N ALA H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS H 299 " --> pdb=" O LYS H 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N SER H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 332 removed outlier: 3.532A pdb=" N MET H 327 " --> pdb=" O THR H 324 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP H 328 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU H 329 " --> pdb=" O MET H 326 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP H 330 " --> pdb=" O MET H 327 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP H 331 " --> pdb=" O ASP H 328 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN H 332 " --> pdb=" O LEU H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 347 removed outlier: 3.738A pdb=" N LYS H 337 " --> pdb=" O PHE H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 365 removed outlier: 3.536A pdb=" N GLY H 360 " --> pdb=" O TRP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 392 removed outlier: 4.105A pdb=" N TYR H 383 " --> pdb=" O ASP H 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA H 384 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 385 " --> pdb=" O ARG H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 397 Processing helix chain 'H' and resid 400 through 418 Processing helix chain 'H' and resid 423 through 441 removed outlier: 3.559A pdb=" N ARG H 427 " --> pdb=" O LEU H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 455 removed outlier: 3.565A pdb=" N ASP H 451 " --> pdb=" O SER H 447 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU H 452 " --> pdb=" O PHE H 448 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS H 453 " --> pdb=" O THR H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 481 removed outlier: 3.822A pdb=" N GLU H 481 " --> pdb=" O HIS H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 484 No H-bonds generated for 'chain 'H' and resid 482 through 484' Processing helix chain 'H' and resid 510 through 530 removed outlier: 4.206A pdb=" N VAL H 516 " --> pdb=" O LYS H 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU H 528 " --> pdb=" O SER H 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG H 529 " --> pdb=" O THR H 525 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 561 removed outlier: 3.689A pdb=" N GLN H 538 " --> pdb=" O ASN H 534 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU H 539 " --> pdb=" O SER H 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS H 540 " --> pdb=" O ILE H 536 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Proline residue: H 543 - end of helix Proline residue: H 556 - end of helix removed outlier: 3.640A pdb=" N LEU H 561 " --> pdb=" O VAL H 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 51 Processing helix chain 'I' and resid 59 through 87 Processing helix chain 'I' and resid 114 through 141 removed outlier: 3.859A pdb=" N TYR I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 163 Processing helix chain 'I' and resid 164 through 168 removed outlier: 3.732A pdb=" N GLU I 167 " --> pdb=" O ASP I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 183 Processing helix chain 'I' and resid 187 through 191 removed outlier: 3.562A pdb=" N HIS I 191 " --> pdb=" O TRP I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 Processing helix chain 'I' and resid 219 through 221 No H-bonds generated for 'chain 'I' and resid 219 through 221' Processing helix chain 'I' and resid 234 through 247 Processing helix chain 'I' and resid 253 through 257 Processing helix chain 'I' and resid 260 through 272 removed outlier: 3.506A pdb=" N LEU I 264 " --> pdb=" O ASP I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 294 removed outlier: 4.331A pdb=" N TRP I 290 " --> pdb=" O ASN I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 298 Processing helix chain 'I' and resid 312 through 320 removed outlier: 3.595A pdb=" N SER I 316 " --> pdb=" O ASN I 312 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 346 Processing helix chain 'I' and resid 353 through 355 No H-bonds generated for 'chain 'I' and resid 353 through 355' Processing helix chain 'I' and resid 356 through 368 Processing helix chain 'I' and resid 370 through 383 removed outlier: 3.595A pdb=" N ASN I 383 " --> pdb=" O SER I 379 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 399 Processing helix chain 'I' and resid 408 through 418 Processing helix chain 'I' and resid 418 through 423 Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 428 through 434 Processing helix chain 'I' and resid 435 through 438 removed outlier: 3.648A pdb=" N PHE I 438 " --> pdb=" O LEU I 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 435 through 438' Processing helix chain 'I' and resid 446 through 457 Processing helix chain 'I' and resid 467 through 482 Processing helix chain 'I' and resid 502 through 515 Processing helix chain 'I' and resid 566 through 570 Processing helix chain 'I' and resid 617 through 621 Processing helix chain 'I' and resid 638 through 644 Processing helix chain 'I' and resid 661 through 665 Processing helix chain 'I' and resid 680 through 687 removed outlier: 3.761A pdb=" N VAL I 684 " --> pdb=" O ASP I 680 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 690 No H-bonds generated for 'chain 'I' and resid 688 through 690' Processing helix chain 'I' and resid 707 through 717 removed outlier: 3.514A pdb=" N LEU I 711 " --> pdb=" O MET I 707 " (cutoff:3.500A) Processing helix chain 'I' and resid 762 through 766 removed outlier: 3.863A pdb=" N ILE I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN I 766 " --> pdb=" O SER I 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 762 through 766' Processing helix chain 'I' and resid 787 through 793 Processing helix chain 'I' and resid 805 through 809 Processing helix chain 'I' and resid 862 through 865 removed outlier: 4.369A pdb=" N SER I 865 " --> pdb=" O LYS I 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 862 through 865' Processing helix chain 'I' and resid 892 through 910 removed outlier: 3.662A pdb=" N GLU I 898 " --> pdb=" O GLU I 894 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N HIS I 910 " --> pdb=" O ALA I 906 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 152 removed outlier: 3.736A pdb=" N ASP J 144 " --> pdb=" O SER J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 158 removed outlier: 4.206A pdb=" N GLN J 157 " --> pdb=" O PHE J 153 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN J 158 " --> pdb=" O PRO J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 165 Processing helix chain 'J' and resid 174 through 203 removed outlier: 4.323A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 226 removed outlier: 3.839A pdb=" N LEU J 213 " --> pdb=" O ASN J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 245 Processing helix chain 'J' and resid 252 through 276 removed outlier: 3.825A pdb=" N SER J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 289 Processing helix chain 'J' and resid 290 through 316 removed outlier: 3.855A pdb=" N ALA J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS J 299 " --> pdb=" O LYS J 295 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR J 305 " --> pdb=" O LYS J 301 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER J 312 " --> pdb=" O LYS J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 332 removed outlier: 3.532A pdb=" N MET J 327 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP J 328 " --> pdb=" O GLU J 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 329 " --> pdb=" O MET J 326 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP J 330 " --> pdb=" O MET J 327 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP J 331 " --> pdb=" O ASP J 328 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN J 332 " --> pdb=" O LEU J 329 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 347 removed outlier: 3.739A pdb=" N LYS J 337 " --> pdb=" O PHE J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 365 removed outlier: 3.536A pdb=" N GLY J 360 " --> pdb=" O TRP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 392 removed outlier: 4.105A pdb=" N TYR J 383 " --> pdb=" O ASP J 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA J 384 " --> pdb=" O GLY J 380 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU J 385 " --> pdb=" O ARG J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 397 Processing helix chain 'J' and resid 400 through 418 Processing helix chain 'J' and resid 423 through 441 removed outlier: 3.559A pdb=" N ARG J 427 " --> pdb=" O LEU J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 455 removed outlier: 3.565A pdb=" N ASP J 451 " --> pdb=" O SER J 447 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU J 452 " --> pdb=" O PHE J 448 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS J 453 " --> pdb=" O THR J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 481 removed outlier: 3.822A pdb=" N GLU J 481 " --> pdb=" O HIS J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 484 No H-bonds generated for 'chain 'J' and resid 482 through 484' Processing helix chain 'J' and resid 510 through 530 removed outlier: 4.207A pdb=" N VAL J 516 " --> pdb=" O LYS J 512 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU J 528 " --> pdb=" O SER J 524 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG J 529 " --> pdb=" O THR J 525 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 561 removed outlier: 3.690A pdb=" N GLN J 538 " --> pdb=" O ASN J 534 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU J 539 " --> pdb=" O SER J 535 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS J 540 " --> pdb=" O ILE J 536 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP J 542 " --> pdb=" O GLN J 538 " (cutoff:3.500A) Proline residue: J 543 - end of helix Proline residue: J 556 - end of helix removed outlier: 3.640A pdb=" N LEU J 561 " --> pdb=" O VAL J 557 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 223 through 228 removed outlier: 3.550A pdb=" N ALA C 225 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS C 194 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 308 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 196 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR C 310 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE C 198 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR C 327 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER C 197 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 444 through 445 removed outlier: 6.494A pdb=" N VAL C 496 " --> pdb=" O ILE C 490 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE C 490 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.885A pdb=" N LEU C 582 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS C 607 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU C 604 " --> pdb=" O ASP C 628 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG C 630 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU C 606 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 627 " --> pdb=" O TYR C 651 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 723 through 725 removed outlier: 6.541A pdb=" N LEU C 724 " --> pdb=" O ALA C 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 731 through 732 removed outlier: 6.728A pdb=" N GLY C 731 " --> pdb=" O TRP C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 778 through 780 removed outlier: 4.591A pdb=" N THR C 858 " --> pdb=" O PHE C 834 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 855 " --> pdb=" O VAL C 883 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP C 885 " --> pdb=" O LEU C 855 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE C 857 " --> pdb=" O ASP C 885 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE C 887 " --> pdb=" O PHE C 857 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 859 " --> pdb=" O ILE C 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 228 removed outlier: 3.550A pdb=" N ALA A 225 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS A 194 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 308 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 196 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR A 310 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 198 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR A 327 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A 197 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.494A pdb=" N VAL A 496 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 490 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.885A pdb=" N LEU A 582 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS A 607 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 604 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG A 630 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 606 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 627 " --> pdb=" O TYR A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 723 through 725 removed outlier: 6.541A pdb=" N LEU A 724 " --> pdb=" O ALA A 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 731 through 732 removed outlier: 6.728A pdb=" N GLY A 731 " --> pdb=" O TRP A 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 778 through 780 removed outlier: 4.591A pdb=" N THR A 858 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 855 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP A 885 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 857 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE A 887 " --> pdb=" O PHE A 857 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE A 859 " --> pdb=" O ILE A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 228 removed outlier: 3.551A pdb=" N ALA E 225 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS E 194 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR E 308 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE E 196 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E 310 " --> pdb=" O ILE E 196 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 198 " --> pdb=" O THR E 310 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR E 327 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER E 197 " --> pdb=" O TYR E 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 444 through 445 removed outlier: 6.495A pdb=" N VAL E 496 " --> pdb=" O ILE E 490 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE E 490 " --> pdb=" O VAL E 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.885A pdb=" N LEU E 582 " --> pdb=" O GLY E 605 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS E 607 " --> pdb=" O LEU E 582 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU E 604 " --> pdb=" O ASP E 628 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG E 630 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU E 606 " --> pdb=" O ARG E 630 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU E 627 " --> pdb=" O TYR E 651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 723 through 725 removed outlier: 6.541A pdb=" N LEU E 724 " --> pdb=" O ALA E 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 731 through 732 removed outlier: 6.728A pdb=" N GLY E 731 " --> pdb=" O TRP E 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 778 through 780 removed outlier: 4.591A pdb=" N THR E 858 " --> pdb=" O PHE E 834 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU E 855 " --> pdb=" O VAL E 883 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP E 885 " --> pdb=" O LEU E 855 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE E 857 " --> pdb=" O ASP E 885 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE E 887 " --> pdb=" O PHE E 857 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE E 859 " --> pdb=" O ILE E 887 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.551A pdb=" N ALA G 225 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS G 194 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR G 308 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 196 " --> pdb=" O THR G 308 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N THR G 310 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE G 198 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR G 327 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER G 197 " --> pdb=" O TYR G 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 444 through 445 removed outlier: 6.495A pdb=" N VAL G 496 " --> pdb=" O ILE G 490 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE G 490 " --> pdb=" O VAL G 496 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 520 through 522 removed outlier: 6.884A pdb=" N LEU G 582 " --> pdb=" O GLY G 605 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS G 607 " --> pdb=" O LEU G 582 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU G 604 " --> pdb=" O ASP G 628 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ARG G 630 " --> pdb=" O LEU G 604 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU G 606 " --> pdb=" O ARG G 630 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU G 627 " --> pdb=" O TYR G 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 723 through 725 removed outlier: 6.541A pdb=" N LEU G 724 " --> pdb=" O ALA G 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'G' and resid 731 through 732 removed outlier: 6.728A pdb=" N GLY G 731 " --> pdb=" O TRP G 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 778 through 780 removed outlier: 4.592A pdb=" N THR G 858 " --> pdb=" O PHE G 834 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU G 855 " --> pdb=" O VAL G 883 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP G 885 " --> pdb=" O LEU G 855 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE G 857 " --> pdb=" O ASP G 885 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE G 887 " --> pdb=" O PHE G 857 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE G 859 " --> pdb=" O ILE G 887 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 223 through 228 removed outlier: 3.550A pdb=" N ALA I 225 " --> pdb=" O LEU I 278 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS I 194 " --> pdb=" O LEU I 306 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR I 308 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE I 196 " --> pdb=" O THR I 308 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR I 310 " --> pdb=" O ILE I 196 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE I 198 " --> pdb=" O THR I 310 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR I 327 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER I 197 " --> pdb=" O TYR I 327 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 444 through 445 removed outlier: 6.495A pdb=" N VAL I 496 " --> pdb=" O ILE I 490 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE I 490 " --> pdb=" O VAL I 496 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 520 through 522 removed outlier: 6.885A pdb=" N LEU I 582 " --> pdb=" O GLY I 605 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS I 607 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU I 604 " --> pdb=" O ASP I 628 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG I 630 " --> pdb=" O LEU I 604 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU I 606 " --> pdb=" O ARG I 630 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 627 " --> pdb=" O TYR I 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 723 through 725 removed outlier: 6.540A pdb=" N LEU I 724 " --> pdb=" O ALA I 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 731 through 732 removed outlier: 6.728A pdb=" N GLY I 731 " --> pdb=" O TRP I 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 778 through 780 removed outlier: 4.592A pdb=" N THR I 858 " --> pdb=" O PHE I 834 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU I 855 " --> pdb=" O VAL I 883 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASP I 885 " --> pdb=" O LEU I 855 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE I 857 " --> pdb=" O ASP I 885 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ILE I 887 " --> pdb=" O PHE I 857 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N PHE I 859 " --> pdb=" O ILE I 887 " (cutoff:3.500A) 2471 hydrogen bonds defined for protein. 6978 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: 18.05 Time building geometry restraints manager: 11.94 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: 11353 1.33 - 1.45: 10968 1.45 - 1.57: 30344 1.57 - 1.69: 35 1.69 - 1.81: 390 Bond restraints: 53090 Sorted by residual: bond pdb=" C4 ATP E1001 " pdb=" C5 ATP E1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.66e+01 bond pdb=" C4 ATP G1001 " pdb=" C5 ATP G1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.64e+01 bond pdb=" C4 ATP I1001 " pdb=" C5 ATP I1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.60e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.57e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.56e+01 ... (remaining 53085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 71316 3.81 - 7.62: 310 7.62 - 11.43: 39 11.43 - 15.25: 5 15.25 - 19.06: 15 Bond angle restraints: 71685 Sorted by residual: angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP C1001 " pdb=" O3B ATP C1001 " pdb=" PG ATP C1001 " ideal model delta sigma weight residual 139.87 120.83 19.04 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP G1001 " pdb=" O3B ATP G1001 " pdb=" PG ATP G1001 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 120.87 19.00 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 ... (remaining 71680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 29403 16.79 - 33.57: 2528 33.57 - 50.36: 498 50.36 - 67.15: 61 67.15 - 83.94: 30 Dihedral angle restraints: 32520 sinusoidal: 13570 harmonic: 18950 Sorted by residual: dihedral pdb=" CA PHE E 346 " pdb=" C PHE E 346 " pdb=" N SER E 347 " pdb=" CA SER E 347 " ideal model delta harmonic sigma weight residual 180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PHE C 346 " pdb=" C PHE C 346 " pdb=" N SER C 347 " pdb=" CA SER C 347 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA PHE I 346 " pdb=" C PHE I 346 " pdb=" N SER I 347 " pdb=" CA SER I 347 " ideal model delta harmonic sigma weight residual -180.00 -150.76 -29.24 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 32517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 6895 0.065 - 0.129: 1112 0.129 - 0.194: 50 0.194 - 0.259: 8 0.259 - 0.323: 5 Chirality restraints: 8070 Sorted by residual: chirality pdb=" CB ILE F 536 " pdb=" CA ILE F 536 " pdb=" CG1 ILE F 536 " pdb=" CG2 ILE F 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE D 536 " pdb=" CA ILE D 536 " pdb=" CG1 ILE D 536 " pdb=" CG2 ILE D 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE B 536 " pdb=" CA ILE B 536 " pdb=" CG1 ILE B 536 " pdb=" CG2 ILE B 536 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 8067 not shown) Planarity restraints: 9035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 441 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASP A 441 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 441 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG A 442 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 441 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C ASP E 441 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP E 441 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG E 442 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 441 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP C 441 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP C 441 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG C 442 " -0.013 2.00e-02 2.50e+03 ... (remaining 9032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 855 2.65 - 3.22: 50255 3.22 - 3.78: 73560 3.78 - 4.34: 102726 4.34 - 4.90: 167562 Nonbonded interactions: 394958 Sorted by model distance: nonbonded pdb=" O HIS H 335 " pdb=" OG1 THR H 338 " model vdw 2.093 3.040 nonbonded pdb=" O HIS F 335 " pdb=" OG1 THR F 338 " model vdw 2.093 3.040 nonbonded pdb=" O HIS J 335 " pdb=" OG1 THR J 338 " model vdw 2.093 3.040 nonbonded pdb=" O HIS B 335 " pdb=" OG1 THR B 338 " model vdw 2.093 3.040 nonbonded pdb=" O HIS D 335 " pdb=" OG1 THR D 338 " model vdw 2.094 3.040 ... (remaining 394953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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: 2.960 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: 0.040 Extract box with map and model: 1.720 Check model and map are aligned: 0.290 Set scattering table: 0.390 Process input model: 88.570 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.220 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 53090 Z= 0.479 Angle : 0.832 19.058 71685 Z= 0.511 Chirality : 0.046 0.323 8070 Planarity : 0.004 0.046 9035 Dihedral : 12.950 83.937 20210 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.80 % Allowed : 5.07 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 6375 helix: -0.41 (0.08), residues: 3135 sheet: -2.03 (0.20), residues: 640 loop : -2.73 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 639 HIS 0.006 0.001 HIS D 487 PHE 0.017 0.002 PHE G 346 TYR 0.015 0.002 TYR D 336 ARG 0.005 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 325 time to evaluate : 4.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 504 MET cc_start: 0.8529 (mmm) cc_final: 0.8305 (mmt) REVERT: E 360 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.8066 (p) REVERT: E 553 MET cc_start: 0.7342 (mtt) cc_final: 0.7098 (mtt) outliers start: 105 outliers final: 25 residues processed: 418 average time/residue: 1.6015 time to fit residues: 812.0009 Evaluate side-chains 202 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 574 SER Chi-restraints excluded: chain E residue 590 SER Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 360 SER Chi-restraints excluded: chain G residue 574 SER Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 360 SER Chi-restraints excluded: chain I residue 574 SER Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 421 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 5.9990 chunk 485 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 327 optimal weight: 0.0470 chunk 259 optimal weight: 3.9990 chunk 501 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 305 optimal weight: 0.5980 chunk 373 optimal weight: 6.9990 chunk 581 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 191 HIS C 255 HIS C 412 GLN C 588 HIS C 739 HIS ** C 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS D 346 ASN D 477 HIS A 130 GLN A 191 HIS A 255 HIS A 412 GLN A 588 HIS A 739 HIS A 846 GLN A 875 HIS B 271 HIS B 332 GLN B 346 ASN B 477 HIS E 130 GLN E 191 HIS E 255 HIS E 412 GLN E 588 HIS E 729 ASN E 739 HIS E 846 GLN F 271 HIS F 346 ASN F 477 HIS G 130 GLN G 191 HIS G 255 HIS G 588 HIS G 739 HIS ** G 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 HIS H 332 GLN H 346 ASN H 432 HIS H 477 HIS I 130 GLN I 191 HIS I 255 HIS I 588 HIS I 739 HIS I 846 GLN J 271 HIS J 332 GLN J 346 ASN J 432 HIS J 477 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 53090 Z= 0.166 Angle : 0.597 14.274 71685 Z= 0.311 Chirality : 0.042 0.169 8070 Planarity : 0.004 0.043 9035 Dihedral : 6.930 85.604 7161 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.30 % Allowed : 9.82 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.11), residues: 6375 helix: 0.87 (0.09), residues: 3180 sheet: -1.27 (0.22), residues: 605 loop : -2.32 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 764 HIS 0.018 0.001 HIS C 739 PHE 0.013 0.001 PHE F 521 TYR 0.011 0.001 TYR G 654 ARG 0.009 0.001 ARG J 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 4.786 Fit side-chains REVERT: C 504 MET cc_start: 0.8469 (mmm) cc_final: 0.8234 (mmt) REVERT: B 136 MET cc_start: 0.6194 (OUTLIER) cc_final: 0.5944 (ttp) REVERT: B 327 MET cc_start: 0.6100 (mtm) cc_final: 0.5780 (mtp) REVERT: B 421 ASN cc_start: 0.6368 (OUTLIER) cc_final: 0.5846 (p0) REVERT: E 386 HIS cc_start: 0.4724 (OUTLIER) cc_final: 0.4519 (m-70) REVERT: I 386 HIS cc_start: 0.4795 (OUTLIER) cc_final: 0.4588 (m-70) REVERT: I 616 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5598 (tmt) outliers start: 76 outliers final: 22 residues processed: 238 average time/residue: 1.3032 time to fit residues: 396.3872 Evaluate side-chains 199 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 386 HIS Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 746 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 483 optimal weight: 8.9990 chunk 395 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 582 optimal weight: 8.9990 chunk 628 optimal weight: 0.0170 chunk 518 optimal weight: 7.9990 chunk 577 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 467 optimal weight: 8.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 HIS C 412 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN A 118 HIS A 412 GLN B 402 HIS E 118 HIS E 412 GLN F 172 GLN G 118 HIS G 729 ASN I 118 HIS I 729 ASN I 846 GLN J 402 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 53090 Z= 0.260 Angle : 0.573 10.032 71685 Z= 0.299 Chirality : 0.042 0.152 8070 Planarity : 0.004 0.039 9035 Dihedral : 6.768 89.715 7120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.53 % Allowed : 10.57 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.11), residues: 6375 helix: 1.31 (0.09), residues: 3155 sheet: -1.20 (0.23), residues: 600 loop : -2.06 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 919 HIS 0.012 0.001 HIS J 487 PHE 0.011 0.001 PHE I 341 TYR 0.016 0.001 TYR E 162 ARG 0.005 0.000 ARG H 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 176 time to evaluate : 4.787 Fit side-chains REVERT: D 327 MET cc_start: 0.6434 (mtm) cc_final: 0.6212 (mtm) REVERT: B 136 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6056 (ttp) REVERT: I 616 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5504 (tmt) outliers start: 89 outliers final: 26 residues processed: 239 average time/residue: 1.2406 time to fit residues: 384.6969 Evaluate side-chains 203 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 616 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 8.9990 chunk 437 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 584 optimal weight: 0.7980 chunk 618 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 553 optimal weight: 3.9990 chunk 166 optimal weight: 0.0030 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 GLN ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN E 875 HIS G 875 HIS I 846 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53090 Z= 0.223 Angle : 0.554 12.872 71685 Z= 0.288 Chirality : 0.042 0.162 8070 Planarity : 0.003 0.038 9035 Dihedral : 6.657 87.778 7120 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.92 % Allowed : 10.66 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 6375 helix: 1.41 (0.09), residues: 3195 sheet: -1.02 (0.24), residues: 575 loop : -2.00 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.004 0.001 HIS J 394 PHE 0.009 0.001 PHE G 834 TYR 0.014 0.001 TYR H 456 ARG 0.005 0.000 ARG J 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 179 time to evaluate : 4.772 Fit side-chains revert: symmetry clash REVERT: C 386 HIS cc_start: 0.4872 (OUTLIER) cc_final: 0.4652 (m-70) REVERT: C 571 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6665 (pt) REVERT: A 386 HIS cc_start: 0.4748 (OUTLIER) cc_final: 0.4527 (m-70) REVERT: B 136 MET cc_start: 0.6273 (OUTLIER) cc_final: 0.6033 (ttp) REVERT: E 386 HIS cc_start: 0.4806 (OUTLIER) cc_final: 0.4590 (m-70) REVERT: I 616 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.5392 (tmt) outliers start: 112 outliers final: 35 residues processed: 259 average time/residue: 1.2136 time to fit residues: 410.4440 Evaluate side-chains 214 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 616 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 6.9990 chunk 351 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 527 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 315 optimal weight: 0.3980 chunk 555 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 412 GLN F 332 GLN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 53090 Z= 0.281 Angle : 0.572 12.075 71685 Z= 0.296 Chirality : 0.042 0.143 8070 Planarity : 0.003 0.064 9035 Dihedral : 6.656 89.364 7120 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.73 % Allowed : 11.53 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6375 helix: 1.52 (0.09), residues: 3180 sheet: -1.00 (0.23), residues: 575 loop : -1.94 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 290 HIS 0.007 0.001 HIS F 335 PHE 0.014 0.001 PHE D 377 TYR 0.015 0.001 TYR E 162 ARG 0.004 0.000 ARG H 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 175 time to evaluate : 4.814 Fit side-chains REVERT: C 386 HIS cc_start: 0.4867 (OUTLIER) cc_final: 0.4653 (m-70) REVERT: C 843 MET cc_start: 0.4329 (OUTLIER) cc_final: 0.4119 (mmt) REVERT: A 386 HIS cc_start: 0.4683 (OUTLIER) cc_final: 0.4451 (m-70) REVERT: E 386 HIS cc_start: 0.5100 (OUTLIER) cc_final: 0.4871 (m-70) REVERT: F 327 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6268 (mtt) REVERT: I 616 MET cc_start: 0.5695 (OUTLIER) cc_final: 0.5382 (tmt) outliers start: 101 outliers final: 44 residues processed: 244 average time/residue: 1.2646 time to fit residues: 397.0335 Evaluate side-chains 225 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 843 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 595 VAL Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 681 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 5.9990 chunk 557 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 363 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 619 optimal weight: 1.9990 chunk 514 optimal weight: 0.8980 chunk 286 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 325 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 ASN D 238 GLN A 729 ASN B 378 GLN E 412 GLN F 432 HIS ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 53090 Z= 0.194 Angle : 0.540 13.453 71685 Z= 0.278 Chirality : 0.041 0.142 8070 Planarity : 0.003 0.044 9035 Dihedral : 6.487 87.331 7120 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.77 % Allowed : 12.08 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 6375 helix: 1.62 (0.09), residues: 3195 sheet: -0.87 (0.24), residues: 575 loop : -1.88 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.006 0.001 HIS B 335 PHE 0.013 0.001 PHE J 376 TYR 0.014 0.001 TYR F 456 ARG 0.004 0.000 ARG F 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 181 time to evaluate : 4.794 Fit side-chains REVERT: C 386 HIS cc_start: 0.4771 (OUTLIER) cc_final: 0.4551 (m-70) REVERT: C 571 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6792 (pt) REVERT: A 386 HIS cc_start: 0.4536 (OUTLIER) cc_final: 0.4268 (m-70) REVERT: F 327 MET cc_start: 0.6406 (mmm) cc_final: 0.6185 (mtt) REVERT: I 616 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.5379 (tmt) outliers start: 103 outliers final: 45 residues processed: 256 average time/residue: 1.2469 time to fit residues: 413.8302 Evaluate side-chains 222 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 4.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 386 HIS Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 379 SER Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain G residue 837 ILE Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 616 MET Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain J residue 509 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 452 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 chunk 521 optimal weight: 0.6980 chunk 345 optimal weight: 20.0000 chunk 616 optimal weight: 8.9990 chunk 386 optimal weight: 0.9990 chunk 376 optimal weight: 40.0000 chunk 284 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 53090 Z= 0.134 Angle : 0.517 12.577 71685 Z= 0.263 Chirality : 0.040 0.143 8070 Planarity : 0.003 0.047 9035 Dihedral : 6.211 87.149 7120 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.46 % Allowed : 12.75 % Favored : 85.79 % 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: 0.27 (0.11), residues: 6375 helix: 1.79 (0.09), residues: 3210 sheet: -0.68 (0.24), residues: 575 loop : -1.76 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 290 HIS 0.007 0.001 HIS F 359 PHE 0.012 0.001 PHE F 376 TYR 0.012 0.001 TYR F 456 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 174 time to evaluate : 4.879 Fit side-chains REVERT: A 199 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8970 (t) REVERT: A 386 HIS cc_start: 0.4596 (OUTLIER) cc_final: 0.4331 (m-70) REVERT: A 837 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6060 (pt) REVERT: E 707 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6469 (ptp) REVERT: F 327 MET cc_start: 0.6374 (mmm) cc_final: 0.6172 (mtt) REVERT: G 571 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6735 (pt) REVERT: H 505 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.4915 (mt) outliers start: 85 outliers final: 35 residues processed: 240 average time/residue: 1.2273 time to fit residues: 383.5813 Evaluate side-chains 211 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 571 LEU Chi-restraints excluded: chain G residue 681 LEU Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 chunk 368 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 392 optimal weight: 0.9990 chunk 420 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 484 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN E 412 GLN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 53090 Z= 0.193 Angle : 0.538 14.389 71685 Z= 0.273 Chirality : 0.041 0.183 8070 Planarity : 0.003 0.046 9035 Dihedral : 6.227 86.145 7120 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.13 % Allowed : 13.32 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 6375 helix: 1.84 (0.09), residues: 3210 sheet: -0.67 (0.24), residues: 575 loop : -1.73 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.006 0.001 HIS D 359 PHE 0.009 0.001 PHE E 834 TYR 0.012 0.001 TYR E 162 ARG 0.003 0.000 ARG J 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 167 time to evaluate : 4.779 Fit side-chains REVERT: A 386 HIS cc_start: 0.4528 (OUTLIER) cc_final: 0.4259 (m-70) REVERT: E 707 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6504 (ptp) REVERT: G 571 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6727 (pt) REVERT: H 307 MET cc_start: 0.7138 (tmm) cc_final: 0.6867 (ppp) REVERT: H 505 ILE cc_start: 0.5345 (OUTLIER) cc_final: 0.4937 (mt) outliers start: 66 outliers final: 42 residues processed: 217 average time/residue: 1.3438 time to fit residues: 370.9656 Evaluate side-chains 212 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 707 MET Chi-restraints excluded: chain E residue 918 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 571 LEU Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain I residue 818 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 4.9990 chunk 590 optimal weight: 0.6980 chunk 539 optimal weight: 5.9990 chunk 574 optimal weight: 6.9990 chunk 345 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 451 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 519 optimal weight: 2.9990 chunk 543 optimal weight: 4.9990 chunk 572 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 53090 Z= 0.162 Angle : 0.534 16.716 71685 Z= 0.269 Chirality : 0.040 0.190 8070 Planarity : 0.003 0.046 9035 Dihedral : 6.174 89.391 7120 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.13 % Allowed : 13.50 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 6375 helix: 1.90 (0.09), residues: 3200 sheet: -0.61 (0.24), residues: 575 loop : -1.69 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.006 0.001 HIS B 335 PHE 0.009 0.001 PHE H 377 TYR 0.014 0.001 TYR J 456 ARG 0.003 0.000 ARG G 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 167 time to evaluate : 4.830 Fit side-chains REVERT: A 386 HIS cc_start: 0.4510 (OUTLIER) cc_final: 0.4245 (m-70) REVERT: B 136 MET cc_start: 0.5374 (tpt) cc_final: 0.5169 (tpt) REVERT: E 707 MET cc_start: 0.6747 (ptp) cc_final: 0.6494 (ptp) REVERT: H 307 MET cc_start: 0.7069 (tmm) cc_final: 0.6781 (ppp) REVERT: H 505 ILE cc_start: 0.5319 (OUTLIER) cc_final: 0.4958 (mp) outliers start: 66 outliers final: 43 residues processed: 220 average time/residue: 1.3394 time to fit residues: 380.6787 Evaluate side-chains 211 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 4.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 918 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain I residue 818 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 1.9990 chunk 607 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 chunk 288 optimal weight: 0.9980 chunk 422 optimal weight: 1.9990 chunk 637 optimal weight: 3.9990 chunk 586 optimal weight: 9.9990 chunk 507 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 392 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 53090 Z= 0.197 Angle : 0.545 15.696 71685 Z= 0.276 Chirality : 0.041 0.183 8070 Planarity : 0.003 0.047 9035 Dihedral : 6.198 89.423 7120 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.94 % Allowed : 13.74 % Favored : 85.31 % 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: 0.43 (0.11), residues: 6375 helix: 1.93 (0.09), residues: 3190 sheet: -0.63 (0.24), residues: 575 loop : -1.67 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.006 0.001 HIS B 335 PHE 0.014 0.001 PHE D 376 TYR 0.017 0.001 TYR B 456 ARG 0.003 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12750 Ramachandran restraints generated. 6375 Oldfield, 0 Emsley, 6375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 169 time to evaluate : 4.821 Fit side-chains REVERT: A 386 HIS cc_start: 0.4882 (OUTLIER) cc_final: 0.4593 (m-70) REVERT: E 707 MET cc_start: 0.6763 (ptp) cc_final: 0.6505 (ptp) REVERT: H 307 MET cc_start: 0.7087 (tmm) cc_final: 0.6741 (ppp) REVERT: H 505 ILE cc_start: 0.5336 (OUTLIER) cc_final: 0.4977 (mp) outliers start: 55 outliers final: 43 residues processed: 213 average time/residue: 1.3359 time to fit residues: 365.9985 Evaluate side-chains 212 residues out of total 5850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 563 SER Chi-restraints excluded: chain E residue 566 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 918 ILE Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 509 HIS Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 563 SER Chi-restraints excluded: chain G residue 707 MET Chi-restraints excluded: chain G residue 712 GLU Chi-restraints excluded: chain G residue 837 ILE Chi-restraints excluded: chain H residue 326 MET Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain I residue 189 SER Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 359 VAL Chi-restraints excluded: chain I residue 563 SER Chi-restraints excluded: chain I residue 595 VAL Chi-restraints excluded: chain I residue 681 LEU Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain J residue 536 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 0.6980 chunk 540 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 468 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 508 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 522 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 93 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 910 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.081407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047760 restraints weight = 177713.542| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.34 r_work: 0.2730 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 53090 Z= 0.151 Angle : 0.538 15.618 71685 Z= 0.269 Chirality : 0.040 0.180 8070 Planarity : 0.003 0.046 9035 Dihedral : 6.093 88.485 7120 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.89 % Allowed : 14.02 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.11), residues: 6375 helix: 1.96 (0.09), residues: 3200 sheet: -0.54 (0.24), residues: 575 loop : -1.64 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 290 HIS 0.006 0.001 HIS B 335 PHE 0.012 0.001 PHE J 376 TYR 0.013 0.001 TYR F 456 ARG 0.003 0.000 ARG D 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9941.33 seconds wall clock time: 173 minutes 54.43 seconds (10434.43 seconds total)