Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 01:23:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wjj_21694/04_2023/6wjj_21694.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 80 5.16 5 C 35880 2.51 5 N 9696 2.21 5 O 11232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 56908 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4144 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "B" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4150 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "L" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5923 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4144 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "F" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4150 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "I" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5923 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4144 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "G" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4150 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "J" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5923 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4144 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "H" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4150 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 500} Chain breaks: 3 Chain: "K" Number of atoms: 5923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5923 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 704} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.33, per 1000 atoms: 0.37 Number of scatterers: 56908 At special positions: 0 Unit cell: (193.67, 193.67, 175.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 80 16.00 O 11232 8.00 N 9696 7.00 C 35880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.91 Conformation dependent library (CDL) restraints added in 7.0 seconds 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13544 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 112 sheets defined 34.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.713A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.502A pdb=" N ASN A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.542A pdb=" N PHE A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.576A pdb=" N GLY A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.608A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 4.178A pdb=" N ILE A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'B' and resid 184 through 191 removed outlier: 3.514A pdb=" N GLU B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 5.238A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 215 " --> pdb=" O HIS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.605A pdb=" N GLY B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.560A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 480 through 487 removed outlier: 4.237A pdb=" N GLU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.621A pdb=" N GLY B 532 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 removed outlier: 3.510A pdb=" N LEU B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.719A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.575A pdb=" N VAL B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 637 Processing helix chain 'L' and resid 31 through 44 Processing helix chain 'L' and resid 51 through 64 removed outlier: 3.519A pdb=" N ALA L 59 " --> pdb=" O LYS L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 77 removed outlier: 3.968A pdb=" N LEU L 71 " --> pdb=" O PRO L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 99 through 101 No H-bonds generated for 'chain 'L' and resid 99 through 101' Processing helix chain 'L' and resid 141 through 158 Processing helix chain 'L' and resid 159 through 163 Processing helix chain 'L' and resid 167 through 179 Processing helix chain 'L' and resid 184 through 190 Processing helix chain 'L' and resid 191 through 196 removed outlier: 3.529A pdb=" N GLU L 196 " --> pdb=" O ASN L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 209 Processing helix chain 'L' and resid 209 through 226 removed outlier: 3.739A pdb=" N VAL L 213 " --> pdb=" O ASN L 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 237 removed outlier: 3.538A pdb=" N ALA L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 250 Processing helix chain 'L' and resid 250 through 262 Processing helix chain 'L' and resid 263 through 278 removed outlier: 3.947A pdb=" N ARG L 267 " --> pdb=" O ARG L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 284 removed outlier: 3.757A pdb=" N SER L 282 " --> pdb=" O TYR L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 298 Processing helix chain 'L' and resid 304 through 309 Processing helix chain 'L' and resid 313 through 321 removed outlier: 3.685A pdb=" N GLU L 317 " --> pdb=" O GLN L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 327 removed outlier: 4.119A pdb=" N SER L 326 " --> pdb=" O GLN L 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER L 327 " --> pdb=" O ILE L 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 323 through 327' Processing helix chain 'L' and resid 331 through 343 removed outlier: 3.827A pdb=" N ILE L 343 " --> pdb=" O LYS L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 381 removed outlier: 4.369A pdb=" N LEU L 381 " --> pdb=" O LYS L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 382 through 384 No H-bonds generated for 'chain 'L' and resid 382 through 384' Processing helix chain 'L' and resid 387 through 396 removed outlier: 3.598A pdb=" N ARG L 391 " --> pdb=" O ASP L 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY L 396 " --> pdb=" O LEU L 392 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 423 Processing helix chain 'L' and resid 442 through 446 removed outlier: 3.576A pdb=" N ASN L 445 " --> pdb=" O ASN L 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 473 Processing helix chain 'L' and resid 551 through 573 removed outlier: 4.135A pdb=" N ILE L 555 " --> pdb=" O PRO L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 610 removed outlier: 3.690A pdb=" N ALA L 599 " --> pdb=" O ILE L 595 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR L 600 " --> pdb=" O VAL L 596 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU L 601 " --> pdb=" O GLU L 597 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE L 610 " --> pdb=" O TRP L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 625 removed outlier: 3.836A pdb=" N ILE L 615 " --> pdb=" O GLN L 611 " (cutoff:3.500A) Processing helix chain 'L' and resid 635 through 639 removed outlier: 4.134A pdb=" N ILE L 639 " --> pdb=" O LEU L 636 " (cutoff:3.500A) Processing helix chain 'L' and resid 679 through 699 removed outlier: 3.607A pdb=" N GLY L 683 " --> pdb=" O ASN L 679 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS L 690 " --> pdb=" O HIS L 686 " (cutoff:3.500A) Processing helix chain 'L' and resid 711 through 721 removed outlier: 3.927A pdb=" N ILE L 715 " --> pdb=" O SER L 711 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP L 716 " --> pdb=" O LYS L 712 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE L 717 " --> pdb=" O LYS L 713 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 744 Processing helix chain 'L' and resid 748 through 759 removed outlier: 3.980A pdb=" N ARG L 752 " --> pdb=" O ASP L 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL L 755 " --> pdb=" O GLU L 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 759 through 770 Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.713A pdb=" N GLU C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS C 213 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 215 " --> pdb=" O HIS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.502A pdb=" N ASN C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.542A pdb=" N PHE C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 485 Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.576A pdb=" N GLY C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 573 through 577 Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.608A pdb=" N VAL C 612 " --> pdb=" O ASP C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 4.178A pdb=" N ILE C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 634 through 638' Processing helix chain 'F' and resid 184 through 191 removed outlier: 3.514A pdb=" N GLU F 188 " --> pdb=" O PRO F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 215 removed outlier: 5.238A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY F 215 " --> pdb=" O HIS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.605A pdb=" N GLY F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 252 removed outlier: 3.560A pdb=" N ARG F 252 " --> pdb=" O PRO F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 487 removed outlier: 4.237A pdb=" N GLU F 486 " --> pdb=" O PRO F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 removed outlier: 3.621A pdb=" N GLY F 532 " --> pdb=" O LYS F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 569 removed outlier: 3.510A pdb=" N LEU F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 577 removed outlier: 3.719A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 617 removed outlier: 3.575A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 637 Processing helix chain 'I' and resid 31 through 44 Processing helix chain 'I' and resid 51 through 64 removed outlier: 3.519A pdb=" N ALA I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.968A pdb=" N LEU I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 141 through 158 Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.529A pdb=" N GLU I 196 " --> pdb=" O ASN I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 Processing helix chain 'I' and resid 209 through 226 removed outlier: 3.739A pdb=" N VAL I 213 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 237 removed outlier: 3.538A pdb=" N ALA I 237 " --> pdb=" O LEU I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 250 through 262 Processing helix chain 'I' and resid 263 through 278 removed outlier: 3.947A pdb=" N ARG I 267 " --> pdb=" O ARG I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 284 removed outlier: 3.757A pdb=" N SER I 282 " --> pdb=" O TYR I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 298 Processing helix chain 'I' and resid 304 through 309 Processing helix chain 'I' and resid 313 through 321 removed outlier: 3.685A pdb=" N GLU I 317 " --> pdb=" O GLN I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 327 removed outlier: 4.119A pdb=" N SER I 326 " --> pdb=" O GLN I 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 327 " --> pdb=" O ILE I 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 323 through 327' Processing helix chain 'I' and resid 331 through 343 removed outlier: 3.827A pdb=" N ILE I 343 " --> pdb=" O LYS I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 381 removed outlier: 4.369A pdb=" N LEU I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 384 No H-bonds generated for 'chain 'I' and resid 382 through 384' Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.598A pdb=" N ARG I 391 " --> pdb=" O ASP I 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY I 396 " --> pdb=" O LEU I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 423 Processing helix chain 'I' and resid 442 through 446 removed outlier: 3.576A pdb=" N ASN I 445 " --> pdb=" O ASN I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 Processing helix chain 'I' and resid 551 through 573 removed outlier: 4.135A pdb=" N ILE I 555 " --> pdb=" O PRO I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 591 through 610 removed outlier: 3.690A pdb=" N ALA I 599 " --> pdb=" O ILE I 595 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR I 600 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU I 601 " --> pdb=" O GLU I 597 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 610 " --> pdb=" O TRP I 606 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 625 removed outlier: 3.836A pdb=" N ILE I 615 " --> pdb=" O GLN I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 635 through 639 removed outlier: 4.134A pdb=" N ILE I 639 " --> pdb=" O LEU I 636 " (cutoff:3.500A) Processing helix chain 'I' and resid 679 through 699 removed outlier: 3.607A pdb=" N GLY I 683 " --> pdb=" O ASN I 679 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS I 690 " --> pdb=" O HIS I 686 " (cutoff:3.500A) Processing helix chain 'I' and resid 711 through 721 removed outlier: 3.927A pdb=" N ILE I 715 " --> pdb=" O SER I 711 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP I 716 " --> pdb=" O LYS I 712 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE I 717 " --> pdb=" O LYS I 713 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 744 Processing helix chain 'I' and resid 748 through 759 removed outlier: 3.980A pdb=" N ARG I 752 " --> pdb=" O ASP I 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL I 755 " --> pdb=" O GLU I 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 770 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.713A pdb=" N GLU D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS D 213 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 215 " --> pdb=" O HIS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.502A pdb=" N ASN D 252 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.542A pdb=" N PHE D 439 " --> pdb=" O ASN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 522 through 532 removed outlier: 3.576A pdb=" N GLY D 532 " --> pdb=" O LYS D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 550 No H-bonds generated for 'chain 'D' and resid 548 through 550' Processing helix chain 'D' and resid 555 through 569 Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.608A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 638 removed outlier: 4.178A pdb=" N ILE D 638 " --> pdb=" O ASP D 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 638' Processing helix chain 'G' and resid 184 through 191 removed outlier: 3.514A pdb=" N GLU G 188 " --> pdb=" O PRO G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 215 removed outlier: 5.238A pdb=" N LYS G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS G 214 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY G 215 " --> pdb=" O HIS G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.605A pdb=" N GLY G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 removed outlier: 3.560A pdb=" N ARG G 252 " --> pdb=" O PRO G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 351 Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 487 removed outlier: 4.237A pdb=" N GLU G 486 " --> pdb=" O PRO G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 removed outlier: 3.621A pdb=" N GLY G 532 " --> pdb=" O LYS G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 569 removed outlier: 3.510A pdb=" N LEU G 569 " --> pdb=" O GLN G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 577 removed outlier: 3.719A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 617 removed outlier: 3.575A pdb=" N VAL G 612 " --> pdb=" O ASP G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 637 Processing helix chain 'J' and resid 31 through 44 Processing helix chain 'J' and resid 51 through 64 removed outlier: 3.519A pdb=" N ALA J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 77 removed outlier: 3.968A pdb=" N LEU J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 141 through 158 Processing helix chain 'J' and resid 159 through 163 Processing helix chain 'J' and resid 167 through 179 Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 191 through 196 removed outlier: 3.529A pdb=" N GLU J 196 " --> pdb=" O ASN J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 209 Processing helix chain 'J' and resid 209 through 226 removed outlier: 3.739A pdb=" N VAL J 213 " --> pdb=" O ASN J 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 237 removed outlier: 3.538A pdb=" N ALA J 237 " --> pdb=" O LEU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 250 Processing helix chain 'J' and resid 250 through 262 Processing helix chain 'J' and resid 263 through 278 removed outlier: 3.947A pdb=" N ARG J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 284 removed outlier: 3.757A pdb=" N SER J 282 " --> pdb=" O TYR J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 298 Processing helix chain 'J' and resid 304 through 309 Processing helix chain 'J' and resid 313 through 321 removed outlier: 3.685A pdb=" N GLU J 317 " --> pdb=" O GLN J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 327 removed outlier: 4.119A pdb=" N SER J 326 " --> pdb=" O GLN J 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER J 327 " --> pdb=" O ILE J 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 323 through 327' Processing helix chain 'J' and resid 331 through 343 removed outlier: 3.827A pdb=" N ILE J 343 " --> pdb=" O LYS J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 381 removed outlier: 4.369A pdb=" N LEU J 381 " --> pdb=" O LYS J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 384 No H-bonds generated for 'chain 'J' and resid 382 through 384' Processing helix chain 'J' and resid 387 through 396 removed outlier: 3.598A pdb=" N ARG J 391 " --> pdb=" O ASP J 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY J 396 " --> pdb=" O LEU J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 423 Processing helix chain 'J' and resid 442 through 446 removed outlier: 3.576A pdb=" N ASN J 445 " --> pdb=" O ASN J 442 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 473 Processing helix chain 'J' and resid 551 through 573 removed outlier: 4.135A pdb=" N ILE J 555 " --> pdb=" O PRO J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 591 through 610 removed outlier: 3.690A pdb=" N ALA J 599 " --> pdb=" O ILE J 595 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR J 600 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU J 601 " --> pdb=" O GLU J 597 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE J 610 " --> pdb=" O TRP J 606 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 625 removed outlier: 3.836A pdb=" N ILE J 615 " --> pdb=" O GLN J 611 " (cutoff:3.500A) Processing helix chain 'J' and resid 635 through 639 removed outlier: 4.134A pdb=" N ILE J 639 " --> pdb=" O LEU J 636 " (cutoff:3.500A) Processing helix chain 'J' and resid 679 through 699 removed outlier: 3.607A pdb=" N GLY J 683 " --> pdb=" O ASN J 679 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS J 690 " --> pdb=" O HIS J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 711 through 721 removed outlier: 3.927A pdb=" N ILE J 715 " --> pdb=" O SER J 711 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP J 716 " --> pdb=" O LYS J 712 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE J 717 " --> pdb=" O LYS J 713 " (cutoff:3.500A) Processing helix chain 'J' and resid 732 through 744 Processing helix chain 'J' and resid 748 through 759 removed outlier: 3.980A pdb=" N ARG J 752 " --> pdb=" O ASP J 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL J 755 " --> pdb=" O GLU J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 770 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.713A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 215 " --> pdb=" O HIS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 248 through 252 removed outlier: 3.502A pdb=" N ASN E 252 " --> pdb=" O PRO E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.542A pdb=" N PHE E 439 " --> pdb=" O ASN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 485 Processing helix chain 'E' and resid 522 through 532 removed outlier: 3.576A pdb=" N GLY E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 550 No H-bonds generated for 'chain 'E' and resid 548 through 550' Processing helix chain 'E' and resid 555 through 569 Processing helix chain 'E' and resid 573 through 577 Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.608A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 638 removed outlier: 4.178A pdb=" N ILE E 638 " --> pdb=" O ASP E 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 634 through 638' Processing helix chain 'H' and resid 184 through 191 removed outlier: 3.514A pdb=" N GLU H 188 " --> pdb=" O PRO H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 215 removed outlier: 5.238A pdb=" N LYS H 213 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY H 215 " --> pdb=" O HIS H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 241 removed outlier: 3.605A pdb=" N GLY H 241 " --> pdb=" O GLU H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 252 removed outlier: 3.560A pdb=" N ARG H 252 " --> pdb=" O PRO H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 351 Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'H' and resid 480 through 487 removed outlier: 4.237A pdb=" N GLU H 486 " --> pdb=" O PRO H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 532 removed outlier: 3.621A pdb=" N GLY H 532 " --> pdb=" O LYS H 528 " (cutoff:3.500A) Processing helix chain 'H' and resid 555 through 569 removed outlier: 3.510A pdb=" N LEU H 569 " --> pdb=" O GLN H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 577 removed outlier: 3.719A pdb=" N THR H 576 " --> pdb=" O ASN H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 617 removed outlier: 3.575A pdb=" N VAL H 612 " --> pdb=" O ASP H 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 637 Processing helix chain 'K' and resid 31 through 44 Processing helix chain 'K' and resid 51 through 64 removed outlier: 3.519A pdb=" N ALA K 59 " --> pdb=" O LYS K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 77 removed outlier: 3.968A pdb=" N LEU K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 99 through 101 No H-bonds generated for 'chain 'K' and resid 99 through 101' Processing helix chain 'K' and resid 141 through 158 Processing helix chain 'K' and resid 159 through 163 Processing helix chain 'K' and resid 167 through 179 Processing helix chain 'K' and resid 184 through 190 Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.529A pdb=" N GLU K 196 " --> pdb=" O ASN K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 209 Processing helix chain 'K' and resid 209 through 226 removed outlier: 3.739A pdb=" N VAL K 213 " --> pdb=" O ASN K 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU K 226 " --> pdb=" O ALA K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 237 removed outlier: 3.538A pdb=" N ALA K 237 " --> pdb=" O LEU K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 250 Processing helix chain 'K' and resid 250 through 262 Processing helix chain 'K' and resid 263 through 278 removed outlier: 3.947A pdb=" N ARG K 267 " --> pdb=" O ARG K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 284 removed outlier: 3.757A pdb=" N SER K 282 " --> pdb=" O TYR K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 298 Processing helix chain 'K' and resid 304 through 309 Processing helix chain 'K' and resid 313 through 321 removed outlier: 3.685A pdb=" N GLU K 317 " --> pdb=" O GLN K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 327 removed outlier: 4.119A pdb=" N SER K 326 " --> pdb=" O GLN K 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER K 327 " --> pdb=" O ILE K 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 323 through 327' Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.827A pdb=" N ILE K 343 " --> pdb=" O LYS K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 381 removed outlier: 4.369A pdb=" N LEU K 381 " --> pdb=" O LYS K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 384 No H-bonds generated for 'chain 'K' and resid 382 through 384' Processing helix chain 'K' and resid 387 through 396 removed outlier: 3.598A pdb=" N ARG K 391 " --> pdb=" O ASP K 387 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 423 Processing helix chain 'K' and resid 442 through 446 removed outlier: 3.576A pdb=" N ASN K 445 " --> pdb=" O ASN K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 473 Processing helix chain 'K' and resid 551 through 573 removed outlier: 4.135A pdb=" N ILE K 555 " --> pdb=" O PRO K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 591 through 610 removed outlier: 3.690A pdb=" N ALA K 599 " --> pdb=" O ILE K 595 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR K 600 " --> pdb=" O VAL K 596 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU K 601 " --> pdb=" O GLU K 597 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE K 610 " --> pdb=" O TRP K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 625 removed outlier: 3.836A pdb=" N ILE K 615 " --> pdb=" O GLN K 611 " (cutoff:3.500A) Processing helix chain 'K' and resid 635 through 639 removed outlier: 4.134A pdb=" N ILE K 639 " --> pdb=" O LEU K 636 " (cutoff:3.500A) Processing helix chain 'K' and resid 679 through 699 removed outlier: 3.607A pdb=" N GLY K 683 " --> pdb=" O ASN K 679 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS K 690 " --> pdb=" O HIS K 686 " (cutoff:3.500A) Processing helix chain 'K' and resid 711 through 721 removed outlier: 3.927A pdb=" N ILE K 715 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP K 716 " --> pdb=" O LYS K 712 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE K 717 " --> pdb=" O LYS K 713 " (cutoff:3.500A) Processing helix chain 'K' and resid 732 through 744 Processing helix chain 'K' and resid 748 through 759 removed outlier: 3.980A pdb=" N ARG K 752 " --> pdb=" O ASP K 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL K 755 " --> pdb=" O GLU K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 770 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 292 removed outlier: 5.219A pdb=" N VAL A 264 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 367 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET A 266 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 365 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 268 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 297 removed outlier: 4.167A pdb=" N ASN A 328 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 452 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 332 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 448 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 392 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 385 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR A 390 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AA6, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.210A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.922A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.674A pdb=" N LEU A 628 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 629 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR A 674 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 3.845A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 696 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 729 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB4, first strand: chain 'B' and resid 289 through 292 removed outlier: 5.209A pdb=" N VAL B 264 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 367 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET B 266 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG B 365 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN B 268 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.590A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 294 through 297 removed outlier: 3.563A pdb=" N ALA B 333 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 296 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 328 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 452 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 392 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 385 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR B 390 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AB8, first strand: chain 'B' and resid 458 through 463 removed outlier: 4.172A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 468 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.825A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AC2, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.723A pdb=" N GLY B 606 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 619 through 622 Processing sheet with id=AC4, first strand: chain 'B' and resid 653 through 655 removed outlier: 3.939A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 700 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 724 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 80 through 84 removed outlier: 3.729A pdb=" N VAL L 128 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AC7, first strand: chain 'L' and resid 436 through 441 removed outlier: 3.581A pdb=" N GLU L 439 " --> pdb=" O TRP L 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 499 " --> pdb=" O MET L 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 549 " --> pdb=" O GLN L 504 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP L 531 " --> pdb=" O ASP L 546 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS L 548 " --> pdb=" O ILE L 529 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE L 529 " --> pdb=" O LYS L 548 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL L 550 " --> pdb=" O LEU L 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU L 527 " --> pdb=" O VAL L 550 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 485 through 487 removed outlier: 3.581A pdb=" N ILE L 520 " --> pdb=" O GLY L 512 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 512 " --> pdb=" O ILE L 520 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 536 through 537 Processing sheet with id=AD1, first strand: chain 'L' and resid 659 through 660 removed outlier: 3.508A pdb=" N SER L 665 " --> pdb=" O VAL L 660 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD3, first strand: chain 'C' and resid 289 through 292 removed outlier: 5.219A pdb=" N VAL C 264 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 367 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET C 266 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG C 365 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN C 268 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 410 through 411 Processing sheet with id=AD5, first strand: chain 'C' and resid 294 through 297 removed outlier: 4.167A pdb=" N ASN C 328 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 452 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 332 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 448 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 392 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 385 " --> pdb=" O THR C 390 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR C 390 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 375 Processing sheet with id=AD7, first strand: chain 'C' and resid 458 through 462 removed outlier: 4.210A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.922A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AE1, first strand: chain 'C' and resid 596 through 598 Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 622 removed outlier: 3.674A pdb=" N LEU C 628 " --> pdb=" O ASN C 621 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 629 " --> pdb=" O THR C 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 674 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 673 " --> pdb=" O ARG C 669 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.845A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL C 696 " --> pdb=" O LYS C 729 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS C 729 " --> pdb=" O VAL C 696 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AE5, first strand: chain 'F' and resid 289 through 292 removed outlier: 5.209A pdb=" N VAL F 264 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 367 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET F 266 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG F 365 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F 268 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 410 through 411 removed outlier: 4.590A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 294 through 297 removed outlier: 3.563A pdb=" N ALA F 333 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 296 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 392 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU F 385 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR F 390 " --> pdb=" O LEU F 385 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 374 through 375 Processing sheet with id=AE9, first strand: chain 'F' and resid 458 through 463 removed outlier: 4.172A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG F 468 " --> pdb=" O ASN F 463 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.825A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AF3, first strand: chain 'F' and resid 596 through 598 removed outlier: 3.723A pdb=" N GLY F 606 " --> pdb=" O HIS F 597 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 619 through 622 Processing sheet with id=AF5, first strand: chain 'F' and resid 653 through 655 removed outlier: 3.939A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 700 " --> pdb=" O ILE F 724 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE F 724 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 80 through 84 removed outlier: 3.729A pdb=" N VAL I 128 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 103 through 105 Processing sheet with id=AF8, first strand: chain 'I' and resid 436 through 441 removed outlier: 3.581A pdb=" N GLU I 439 " --> pdb=" O TRP I 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 499 " --> pdb=" O MET I 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL I 549 " --> pdb=" O GLN I 504 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP I 531 " --> pdb=" O ASP I 546 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS I 548 " --> pdb=" O ILE I 529 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE I 529 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL I 550 " --> pdb=" O LEU I 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU I 527 " --> pdb=" O VAL I 550 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 485 through 487 removed outlier: 3.581A pdb=" N ILE I 520 " --> pdb=" O GLY I 512 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY I 512 " --> pdb=" O ILE I 520 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 536 through 537 Processing sheet with id=AG2, first strand: chain 'I' and resid 659 through 660 removed outlier: 3.508A pdb=" N SER I 665 " --> pdb=" O VAL I 660 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AG4, first strand: chain 'D' and resid 289 through 292 removed outlier: 5.219A pdb=" N VAL D 264 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL D 367 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET D 266 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG D 365 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 268 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 410 through 411 Processing sheet with id=AG6, first strand: chain 'D' and resid 294 through 297 removed outlier: 4.167A pdb=" N ASN D 328 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 452 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 332 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 448 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 392 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU D 385 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR D 390 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 374 through 375 Processing sheet with id=AG8, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.210A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.922A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AH2, first strand: chain 'D' and resid 596 through 598 Processing sheet with id=AH3, first strand: chain 'D' and resid 619 through 622 removed outlier: 3.674A pdb=" N LEU D 628 " --> pdb=" O ASN D 621 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 629 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 674 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 673 " --> pdb=" O ARG D 669 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 653 through 655 removed outlier: 3.845A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL D 696 " --> pdb=" O LYS D 729 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS D 729 " --> pdb=" O VAL D 696 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH6, first strand: chain 'G' and resid 289 through 292 removed outlier: 5.209A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 410 through 411 removed outlier: 4.590A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 294 through 297 removed outlier: 3.563A pdb=" N ALA G 333 " --> pdb=" O SER G 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER G 296 " --> pdb=" O THR G 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 374 through 375 Processing sheet with id=AI1, first strand: chain 'G' and resid 458 through 463 removed outlier: 4.172A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG G 468 " --> pdb=" O ASN G 463 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.825A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AI4, first strand: chain 'G' and resid 596 through 598 removed outlier: 3.723A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 619 through 622 Processing sheet with id=AI6, first strand: chain 'G' and resid 653 through 655 removed outlier: 3.939A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA G 700 " --> pdb=" O ILE G 724 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE G 724 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 80 through 84 removed outlier: 3.729A pdb=" N VAL J 128 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AI9, first strand: chain 'J' and resid 436 through 441 removed outlier: 3.581A pdb=" N GLU J 439 " --> pdb=" O TRP J 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 499 " --> pdb=" O MET J 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL J 549 " --> pdb=" O GLN J 504 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP J 531 " --> pdb=" O ASP J 546 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS J 548 " --> pdb=" O ILE J 529 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE J 529 " --> pdb=" O LYS J 548 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL J 550 " --> pdb=" O LEU J 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU J 527 " --> pdb=" O VAL J 550 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 485 through 487 removed outlier: 3.581A pdb=" N ILE J 520 " --> pdb=" O GLY J 512 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY J 512 " --> pdb=" O ILE J 520 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 536 through 537 Processing sheet with id=AJ3, first strand: chain 'J' and resid 659 through 660 removed outlier: 3.508A pdb=" N SER J 665 " --> pdb=" O VAL J 660 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AJ5, first strand: chain 'E' and resid 289 through 292 removed outlier: 5.219A pdb=" N VAL E 264 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL E 367 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET E 266 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG E 365 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN E 268 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 410 through 411 Processing sheet with id=AJ7, first strand: chain 'E' and resid 294 through 297 removed outlier: 4.167A pdb=" N ASN E 328 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 452 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 332 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 448 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 392 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU E 385 " --> pdb=" O THR E 390 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR E 390 " --> pdb=" O LEU E 385 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 374 through 375 Processing sheet with id=AJ9, first strand: chain 'E' and resid 458 through 462 removed outlier: 4.210A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.922A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AK3, first strand: chain 'E' and resid 596 through 598 Processing sheet with id=AK4, first strand: chain 'E' and resid 619 through 622 removed outlier: 3.674A pdb=" N LEU E 628 " --> pdb=" O ASN E 621 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 629 " --> pdb=" O THR E 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR E 674 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 673 " --> pdb=" O ARG E 669 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 653 through 655 removed outlier: 3.845A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 696 " --> pdb=" O LYS E 729 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 729 " --> pdb=" O VAL E 696 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 192 through 196 Processing sheet with id=AK7, first strand: chain 'H' and resid 289 through 292 removed outlier: 5.209A pdb=" N VAL H 264 " --> pdb=" O VAL H 367 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL H 367 " --> pdb=" O VAL H 264 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET H 266 " --> pdb=" O ARG H 365 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG H 365 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN H 268 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 410 through 411 removed outlier: 4.590A pdb=" N ILE H 432 " --> pdb=" O LEU H 360 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 294 through 297 removed outlier: 3.563A pdb=" N ALA H 333 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 296 " --> pdb=" O THR H 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA H 392 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU H 385 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N THR H 390 " --> pdb=" O LEU H 385 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 374 through 375 Processing sheet with id=AL2, first strand: chain 'H' and resid 458 through 463 removed outlier: 4.172A pdb=" N ILE H 459 " --> pdb=" O ASP H 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG H 468 " --> pdb=" O ASN H 463 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'H' and resid 501 through 506 removed outlier: 8.825A pdb=" N ILE H 589 " --> pdb=" O THR H 488 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG H 490 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE H 591 " --> pdb=" O ARG H 490 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE H 492 " --> pdb=" O ILE H 591 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASP H 593 " --> pdb=" O ILE H 492 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 541 through 542 Processing sheet with id=AL5, first strand: chain 'H' and resid 596 through 598 removed outlier: 3.723A pdb=" N GLY H 606 " --> pdb=" O HIS H 597 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'H' and resid 619 through 622 Processing sheet with id=AL7, first strand: chain 'H' and resid 653 through 655 removed outlier: 3.939A pdb=" N GLY H 641 " --> pdb=" O VAL H 701 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 700 " --> pdb=" O ILE H 724 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE H 724 " --> pdb=" O ALA H 700 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 80 through 84 removed outlier: 3.729A pdb=" N VAL K 128 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 103 through 105 Processing sheet with id=AM1, first strand: chain 'K' and resid 436 through 441 removed outlier: 3.581A pdb=" N GLU K 439 " --> pdb=" O TRP K 501 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU K 499 " --> pdb=" O MET K 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 549 " --> pdb=" O GLN K 504 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP K 531 " --> pdb=" O ASP K 546 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS K 548 " --> pdb=" O ILE K 529 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE K 529 " --> pdb=" O LYS K 548 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL K 550 " --> pdb=" O LEU K 527 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU K 527 " --> pdb=" O VAL K 550 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 485 through 487 removed outlier: 3.581A pdb=" N ILE K 520 " --> pdb=" O GLY K 512 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY K 512 " --> pdb=" O ILE K 520 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 536 through 537 Processing sheet with id=AM4, first strand: chain 'K' and resid 659 through 660 removed outlier: 3.508A pdb=" N SER K 665 " --> pdb=" O VAL K 660 " (cutoff:3.500A) 1954 hydrogen bonds defined for protein. 5445 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: 19.54 Time building geometry restraints manager: 18.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 16536 1.33 - 1.45: 8516 1.45 - 1.57: 32656 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 57860 Sorted by residual: bond pdb=" N LEU L 576 " pdb=" CA LEU L 576 " ideal model delta sigma weight residual 1.455 1.492 -0.036 7.00e-03 2.04e+04 2.71e+01 bond pdb=" N LEU K 576 " pdb=" CA LEU K 576 " ideal model delta sigma weight residual 1.455 1.492 -0.036 7.00e-03 2.04e+04 2.71e+01 bond pdb=" N LEU J 576 " pdb=" CA LEU J 576 " ideal model delta sigma weight residual 1.455 1.492 -0.036 7.00e-03 2.04e+04 2.71e+01 bond pdb=" N LEU I 576 " pdb=" CA LEU I 576 " ideal model delta sigma weight residual 1.455 1.492 -0.036 7.00e-03 2.04e+04 2.71e+01 bond pdb=" CA ARG I 321 " pdb=" CB ARG I 321 " ideal model delta sigma weight residual 1.528 1.569 -0.041 1.39e-02 5.18e+03 8.71e+00 ... (remaining 57855 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.64: 960 105.64 - 112.81: 30515 112.81 - 119.98: 21383 119.98 - 127.15: 24914 127.15 - 134.32: 480 Bond angle restraints: 78252 Sorted by residual: angle pdb=" N ILE G 726 " pdb=" CA ILE G 726 " pdb=" C ILE G 726 " ideal model delta sigma weight residual 112.17 106.35 5.82 9.50e-01 1.11e+00 3.76e+01 angle pdb=" N ILE H 726 " pdb=" CA ILE H 726 " pdb=" C ILE H 726 " ideal model delta sigma weight residual 112.17 106.35 5.82 9.50e-01 1.11e+00 3.76e+01 angle pdb=" N ILE F 726 " pdb=" CA ILE F 726 " pdb=" C ILE F 726 " ideal model delta sigma weight residual 112.17 106.35 5.82 9.50e-01 1.11e+00 3.76e+01 angle pdb=" N ILE B 726 " pdb=" CA ILE B 726 " pdb=" C ILE B 726 " ideal model delta sigma weight residual 112.17 106.35 5.82 9.50e-01 1.11e+00 3.76e+01 angle pdb=" C LEU J 505 " pdb=" N SER J 506 " pdb=" CA SER J 506 " ideal model delta sigma weight residual 123.15 134.13 -10.98 2.23e+00 2.01e-01 2.42e+01 ... (remaining 78247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 33435 15.77 - 31.53: 1658 31.53 - 47.30: 343 47.30 - 63.06: 36 63.06 - 78.83: 32 Dihedral angle restraints: 35504 sinusoidal: 14620 harmonic: 20884 Sorted by residual: dihedral pdb=" CA TYR E 699 " pdb=" C TYR E 699 " pdb=" N ALA E 700 " pdb=" CA ALA E 700 " ideal model delta harmonic sigma weight residual 180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA TYR A 699 " pdb=" C TYR A 699 " pdb=" N ALA A 700 " pdb=" CA ALA A 700 " ideal model delta harmonic sigma weight residual -180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA TYR D 699 " pdb=" C TYR D 699 " pdb=" N ALA D 700 " pdb=" CA ALA D 700 " ideal model delta harmonic sigma weight residual -180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 35501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 7284 0.080 - 0.161: 1436 0.161 - 0.241: 116 0.241 - 0.322: 12 0.322 - 0.402: 4 Chirality restraints: 8852 Sorted by residual: chirality pdb=" CA SER F 327 " pdb=" N SER F 327 " pdb=" C SER F 327 " pdb=" CB SER F 327 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA SER H 327 " pdb=" N SER H 327 " pdb=" C SER H 327 " pdb=" CB SER H 327 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA SER G 327 " pdb=" N SER G 327 " pdb=" C SER G 327 " pdb=" CB SER G 327 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 8849 not shown) Planarity restraints: 10148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 512 " 0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO B 513 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 513 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 513 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 512 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO G 513 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 513 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 513 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 512 " 0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO F 513 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 513 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 513 " 0.047 5.00e-02 4.00e+02 ... (remaining 10145 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2754 2.71 - 3.26: 51317 3.26 - 3.81: 85491 3.81 - 4.35: 107865 4.35 - 4.90: 184893 Nonbonded interactions: 432320 Sorted by model distance: nonbonded pdb=" O TYR I 728 " pdb="ZN ZN I 802 " model vdw 2.163 2.230 nonbonded pdb=" O TYR L 728 " pdb="ZN ZN L 802 " model vdw 2.163 2.230 nonbonded pdb=" O TYR K 728 " pdb="ZN ZN K 802 " model vdw 2.163 2.230 nonbonded pdb=" O TYR J 728 " pdb="ZN ZN J 802 " model vdw 2.163 2.230 nonbonded pdb=" O ASN L 586 " pdb=" OG1 THR L 632 " model vdw 2.243 2.440 ... (remaining 432315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 274 or resid 286 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'B' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 301 or resid 326 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'C' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 274 or resid 286 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'D' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 274 or resid 286 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'E' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 274 or resid 286 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'F' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 301 or resid 326 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'G' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 301 or resid 326 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) selection = (chain 'H' and (resid 174 through 244 or resid 246 through 251 or resid 253 thro \ ugh 301 or resid 326 through 511 or resid 513 through 735 or resid 801 through 8 \ 02)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 9.600 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 109.040 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.008 0.099 57860 Z= 0.541 Angle : 1.046 12.093 78252 Z= 0.609 Chirality : 0.062 0.402 8852 Planarity : 0.007 0.083 10148 Dihedral : 10.437 78.830 21960 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.84 % 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: -3.43 (0.08), residues: 6996 helix: -2.79 (0.08), residues: 2164 sheet: -0.96 (0.14), residues: 1152 loop : -2.39 (0.08), residues: 3680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1010 time to evaluate : 5.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 33 residues processed: 1063 average time/residue: 0.5955 time to fit residues: 1021.4696 Evaluate side-chains 438 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 405 time to evaluate : 5.216 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4704 time to fit residues: 34.5695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 594 optimal weight: 4.9990 chunk 533 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 359 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 551 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 335 optimal weight: 2.9990 chunk 410 optimal weight: 2.9990 chunk 639 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 263 HIS A 363 ASN A 409 ASN A 537 ASN A 541 GLN B 263 HIS B 363 ASN B 409 ASN B 463 ASN B 697 ASN L 32 GLN L 117 HIS L 253 ASN L 279 GLN L 440 ASN L 444 ASN L 563 GLN L 567 ASN L 571 ASN L 586 ASN L 594 ASN L 769 GLN C 246 ASN C 263 HIS C 363 ASN C 409 ASN C 537 ASN C 541 GLN F 263 HIS F 363 ASN F 409 ASN F 463 ASN F 697 ASN I 32 GLN I 117 HIS I 253 ASN I 279 GLN I 440 ASN I 444 ASN I 563 GLN I 567 ASN I 571 ASN I 586 ASN I 594 ASN I 642 GLN I 769 GLN D 246 ASN D 263 HIS D 363 ASN D 409 ASN D 537 ASN D 541 GLN G 263 HIS G 292 ASN G 363 ASN G 409 ASN G 463 ASN G 697 ASN J 32 GLN J 117 HIS J 253 ASN J 279 GLN J 440 ASN J 444 ASN J 563 GLN J 567 ASN J 571 ASN J 586 ASN J 594 ASN J 642 GLN J 769 GLN E 246 ASN E 263 HIS E 363 ASN E 409 ASN E 537 ASN E 541 GLN H 263 HIS H 363 ASN H 409 ASN H 463 ASN H 697 ASN K 32 GLN K 117 HIS K 253 ASN K 279 GLN K 440 ASN K 444 ASN K 563 GLN K 567 ASN K 571 ASN K 586 ASN K 594 ASN K 769 GLN Total number of N/Q/H flips: 95 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 57860 Z= 0.174 Angle : 0.549 7.340 78252 Z= 0.298 Chirality : 0.045 0.166 8852 Planarity : 0.005 0.042 10148 Dihedral : 5.303 23.171 7596 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -2.01 (0.09), residues: 6996 helix: -1.08 (0.10), residues: 2212 sheet: -0.51 (0.15), residues: 1192 loop : -1.77 (0.09), residues: 3592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 517 time to evaluate : 5.283 Fit side-chains outliers start: 93 outliers final: 44 residues processed: 590 average time/residue: 0.5452 time to fit residues: 543.2628 Evaluate side-chains 417 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 373 time to evaluate : 5.175 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.3895 time to fit residues: 40.3036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 355 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 532 optimal weight: 8.9990 chunk 435 optimal weight: 0.0970 chunk 176 optimal weight: 10.0000 chunk 640 optimal weight: 6.9990 chunk 691 optimal weight: 5.9990 chunk 570 optimal weight: 0.0980 chunk 635 optimal weight: 4.9990 chunk 218 optimal weight: 0.0170 chunk 513 optimal weight: 9.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 GLN L 115 HIS L 586 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 115 HIS I 586 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN J 115 HIS J 586 ASN ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN K 115 HIS K 586 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 57860 Z= 0.119 Angle : 0.481 6.828 78252 Z= 0.256 Chirality : 0.043 0.134 8852 Planarity : 0.004 0.048 10148 Dihedral : 4.544 19.931 7596 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.10), residues: 6996 helix: -0.12 (0.11), residues: 2172 sheet: -0.13 (0.15), residues: 1260 loop : -1.25 (0.10), residues: 3564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 490 time to evaluate : 5.280 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 outliers start: 100 outliers final: 32 residues processed: 582 average time/residue: 0.5317 time to fit residues: 532.9428 Evaluate side-chains 400 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 368 time to evaluate : 6.050 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4197 time to fit residues: 33.8989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 632 optimal weight: 0.0870 chunk 481 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 305 optimal weight: 9.9990 chunk 430 optimal weight: 0.0020 chunk 642 optimal weight: 6.9990 chunk 680 optimal weight: 9.9990 chunk 335 optimal weight: 6.9990 chunk 609 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN ** E 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 57860 Z= 0.110 Angle : 0.465 7.806 78252 Z= 0.247 Chirality : 0.043 0.194 8852 Planarity : 0.003 0.048 10148 Dihedral : 4.223 18.675 7596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.55 (0.10), residues: 6996 helix: 0.38 (0.11), residues: 2172 sheet: 0.17 (0.15), residues: 1232 loop : -1.00 (0.10), residues: 3592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 430 time to evaluate : 5.162 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 outliers start: 64 outliers final: 24 residues processed: 478 average time/residue: 0.5234 time to fit residues: 433.1726 Evaluate side-chains 384 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 360 time to evaluate : 5.175 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3872 time to fit residues: 25.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 566 optimal weight: 9.9990 chunk 386 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 506 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 470 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 30.0000 chunk 610 optimal weight: 7.9990 chunk 171 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN B 211 HIS ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 642 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN F 211 HIS ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 HIS ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 HIS ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 642 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 57860 Z= 0.436 Angle : 0.652 7.683 78252 Z= 0.346 Chirality : 0.050 0.177 8852 Planarity : 0.004 0.045 10148 Dihedral : 5.125 21.052 7596 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.10), residues: 6996 helix: 0.06 (0.11), residues: 2216 sheet: -0.21 (0.15), residues: 1200 loop : -1.36 (0.10), residues: 3580 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 421 time to evaluate : 6.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 130 outliers final: 58 residues processed: 523 average time/residue: 0.5355 time to fit residues: 481.9676 Evaluate side-chains 410 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 352 time to evaluate : 5.223 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3879 time to fit residues: 50.8553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 228 optimal weight: 8.9990 chunk 612 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 399 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 681 optimal weight: 8.9990 chunk 565 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 357 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN L 211 ASN ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN J 211 ASN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN K 211 ASN K 297 GLN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 57860 Z= 0.332 Angle : 0.578 7.982 78252 Z= 0.306 Chirality : 0.047 0.188 8852 Planarity : 0.004 0.047 10148 Dihedral : 4.963 20.382 7596 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 6996 helix: 0.11 (0.11), residues: 2204 sheet: -0.39 (0.15), residues: 1172 loop : -1.36 (0.10), residues: 3620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 364 time to evaluate : 5.295 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 outliers start: 83 outliers final: 52 residues processed: 435 average time/residue: 0.5227 time to fit residues: 397.8239 Evaluate side-chains 379 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 327 time to evaluate : 5.196 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.4128 time to fit residues: 48.5010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 656 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 497 optimal weight: 5.9990 chunk 385 optimal weight: 5.9990 chunk 573 optimal weight: 0.9980 chunk 380 optimal weight: 1.9990 chunk 678 optimal weight: 0.0870 chunk 424 optimal weight: 0.0000 chunk 413 optimal weight: 2.9990 chunk 313 optimal weight: 4.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN L 297 GLN ** L 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 745 HIS C 361 ASN I 297 GLN ** I 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 745 HIS D 361 ASN J 297 GLN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 57860 Z= 0.125 Angle : 0.475 7.977 78252 Z= 0.253 Chirality : 0.044 0.257 8852 Planarity : 0.003 0.049 10148 Dihedral : 4.322 19.224 7596 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.54 (0.10), residues: 6996 helix: 0.62 (0.11), residues: 2156 sheet: -0.20 (0.15), residues: 1220 loop : -1.00 (0.10), residues: 3620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 367 time to evaluate : 5.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 401 average time/residue: 0.5259 time to fit residues: 370.2464 Evaluate side-chains 366 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 339 time to evaluate : 5.183 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4041 time to fit residues: 28.4040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 419 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 131 optimal weight: 0.0020 chunk 431 optimal weight: 5.9990 chunk 462 optimal weight: 10.0000 chunk 335 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 533 optimal weight: 0.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 ASN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 57860 Z= 0.176 Angle : 0.490 7.789 78252 Z= 0.259 Chirality : 0.044 0.169 8852 Planarity : 0.003 0.050 10148 Dihedral : 4.293 18.906 7596 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.42 (0.10), residues: 6996 helix: 0.73 (0.11), residues: 2164 sheet: -0.04 (0.15), residues: 1184 loop : -0.97 (0.10), residues: 3648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 351 time to evaluate : 5.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 1 residues processed: 378 average time/residue: 0.5362 time to fit residues: 354.7829 Evaluate side-chains 338 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 5.344 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4043 time to fit residues: 8.2065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 617 optimal weight: 9.9990 chunk 650 optimal weight: 5.9990 chunk 593 optimal weight: 7.9990 chunk 632 optimal weight: 0.0040 chunk 649 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 496 optimal weight: 8.9990 chunk 194 optimal weight: 0.0270 chunk 571 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 overall best weight: 3.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 57860 Z= 0.284 Angle : 0.549 7.591 78252 Z= 0.290 Chirality : 0.046 0.165 8852 Planarity : 0.004 0.050 10148 Dihedral : 4.639 18.791 7596 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.59 (0.10), residues: 6996 helix: 0.57 (0.11), residues: 2192 sheet: -0.26 (0.15), residues: 1260 loop : -1.03 (0.10), residues: 3544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 361 time to evaluate : 5.652 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 outliers start: 31 outliers final: 19 residues processed: 380 average time/residue: 0.5396 time to fit residues: 358.4131 Evaluate side-chains 353 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 334 time to evaluate : 5.228 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3991 time to fit residues: 21.9958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 630 optimal weight: 3.9990 chunk 415 optimal weight: 10.0000 chunk 668 optimal weight: 7.9990 chunk 408 optimal weight: 0.9980 chunk 317 optimal weight: 6.9990 chunk 464 optimal weight: 4.9990 chunk 701 optimal weight: 7.9990 chunk 645 optimal weight: 0.9990 chunk 558 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 431 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 57860 Z= 0.138 Angle : 0.474 7.640 78252 Z= 0.252 Chirality : 0.044 0.169 8852 Planarity : 0.003 0.049 10148 Dihedral : 4.268 19.322 7596 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.28 (0.10), residues: 6996 helix: 0.84 (0.11), residues: 2164 sheet: 0.06 (0.15), residues: 1220 loop : -0.89 (0.10), residues: 3612 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13992 Ramachandran restraints generated. 6996 Oldfield, 0 Emsley, 6996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 369 time to evaluate : 5.316 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 outliers start: 5 outliers final: 1 residues processed: 370 average time/residue: 0.5386 time to fit residues: 348.7186 Evaluate side-chains 338 residues out of total 6412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 5.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3980 time to fit residues: 8.1010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 342 optimal weight: 0.0970 chunk 443 optimal weight: 9.9990 chunk 594 optimal weight: 7.9990 chunk 171 optimal weight: 0.0670 chunk 514 optimal weight: 0.9980 chunk 82 optimal weight: 0.0170 chunk 155 optimal weight: 3.9990 chunk 559 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 574 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 709 ASN ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 709 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 709 ASN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 709 ASN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.163549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130370 restraints weight = 91768.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127603 restraints weight = 166630.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128548 restraints weight = 146464.043| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 57860 Z= 0.110 Angle : 0.456 7.677 78252 Z= 0.240 Chirality : 0.043 0.169 8852 Planarity : 0.003 0.048 10148 Dihedral : 3.904 17.965 7596 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % 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: -0.01 (0.10), residues: 6996 helix: 1.17 (0.12), residues: 2140 sheet: -0.01 (0.15), residues: 1280 loop : -0.70 (0.10), residues: 3576 =============================================================================== Job complete usr+sys time: 8886.70 seconds wall clock time: 159 minutes 52.59 seconds (9592.59 seconds total)