Starting phenix.real_space_refine on Sun Dec 29 10:37:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_21694.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_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/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_21694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_21694.map" model { file = "/net/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_21694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wjj_21694/12_2024/6wjj_21694.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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. Time to flip 4 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 22.98, per 1000 atoms: 0.40 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.84 Conformation dependent library (CDL) restraints added in 5.6 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: 6.59 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: 26.40 Time building geometry restraints manager: 12.85 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: 0.00 - 2.42: 75298 2.42 - 4.84: 2658 4.84 - 7.26: 244 7.26 - 9.67: 40 9.67 - 12.09: 12 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 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.680 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 104.630 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.440 ------------------------------------------------------------------------------- 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 % Allowed : 3.18 % Favored : 95.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP J 281 HIS 0.009 0.002 HIS J 745 PHE 0.037 0.003 PHE J 190 TYR 0.041 0.004 TYR K 148 ARG 0.010 0.001 ARG I 502 *********************** 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 to be fit. rotamer outliers: 57 poor density : 1010 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.8244 (ttm) cc_final: 0.7893 (ttt) REVERT: A 350 MET cc_start: 0.7760 (mtp) cc_final: 0.7420 (mtp) REVERT: A 576 THR cc_start: 0.8948 (p) cc_final: 0.8681 (t) REVERT: B 195 ASP cc_start: 0.8339 (t0) cc_final: 0.7861 (p0) REVERT: B 501 VAL cc_start: 0.9479 (t) cc_final: 0.9277 (m) REVERT: B 521 MET cc_start: 0.8856 (tpp) cc_final: 0.8571 (tpp) REVERT: B 587 MET cc_start: 0.8778 (mtt) cc_final: 0.8274 (mtt) REVERT: B 662 MET cc_start: 0.6543 (mtm) cc_final: 0.6305 (mtm) REVERT: L 267 ARG cc_start: 0.5885 (mtp85) cc_final: 0.5627 (mtp180) REVERT: L 290 ARG cc_start: 0.5629 (mtm-85) cc_final: 0.5394 (mtt180) REVERT: L 515 GLU cc_start: 0.5569 (mm-30) cc_final: 0.4972 (pm20) REVERT: L 649 ILE cc_start: 0.3742 (OUTLIER) cc_final: 0.3537 (mm) REVERT: C 266 MET cc_start: 0.8239 (ttm) cc_final: 0.7886 (ttt) REVERT: C 350 MET cc_start: 0.7749 (mtp) cc_final: 0.7413 (mtp) REVERT: C 576 THR cc_start: 0.8948 (p) cc_final: 0.8684 (t) REVERT: F 195 ASP cc_start: 0.8338 (t0) cc_final: 0.7862 (p0) REVERT: F 521 MET cc_start: 0.8859 (tpp) cc_final: 0.8574 (tpp) REVERT: F 587 MET cc_start: 0.8778 (mtt) cc_final: 0.8274 (mtt) REVERT: F 662 MET cc_start: 0.6556 (mtm) cc_final: 0.6322 (mtm) REVERT: I 267 ARG cc_start: 0.5884 (mtp85) cc_final: 0.5621 (mtp180) REVERT: I 290 ARG cc_start: 0.5623 (mtm-85) cc_final: 0.5388 (mtt180) REVERT: I 515 GLU cc_start: 0.5572 (mm-30) cc_final: 0.4973 (pm20) REVERT: I 649 ILE cc_start: 0.3741 (OUTLIER) cc_final: 0.3535 (mm) REVERT: D 266 MET cc_start: 0.8243 (ttm) cc_final: 0.7887 (ttt) REVERT: D 350 MET cc_start: 0.7749 (mtp) cc_final: 0.7415 (mtp) REVERT: D 576 THR cc_start: 0.8948 (p) cc_final: 0.8684 (t) REVERT: G 195 ASP cc_start: 0.8337 (t0) cc_final: 0.7856 (p0) REVERT: G 521 MET cc_start: 0.8866 (tpp) cc_final: 0.8583 (tpp) REVERT: G 587 MET cc_start: 0.8783 (mtt) cc_final: 0.8274 (mtt) REVERT: G 662 MET cc_start: 0.6550 (mtm) cc_final: 0.6313 (mtm) REVERT: J 267 ARG cc_start: 0.5888 (mtp85) cc_final: 0.5627 (mtp180) REVERT: J 290 ARG cc_start: 0.5623 (mtm-85) cc_final: 0.5388 (mtt180) REVERT: J 515 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4975 (pm20) REVERT: J 649 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3538 (mm) REVERT: E 266 MET cc_start: 0.8242 (ttm) cc_final: 0.7889 (ttt) REVERT: E 350 MET cc_start: 0.7755 (mtp) cc_final: 0.7416 (mtp) REVERT: E 576 THR cc_start: 0.8948 (p) cc_final: 0.8679 (t) REVERT: H 195 ASP cc_start: 0.8339 (t0) cc_final: 0.7853 (p0) REVERT: H 521 MET cc_start: 0.8864 (tpp) cc_final: 0.8585 (tpp) REVERT: H 587 MET cc_start: 0.8785 (mtt) cc_final: 0.8276 (mtt) REVERT: H 662 MET cc_start: 0.6542 (mtm) cc_final: 0.6306 (mtm) REVERT: K 267 ARG cc_start: 0.5887 (mtp85) cc_final: 0.5629 (mtp180) REVERT: K 290 ARG cc_start: 0.5624 (mtm-85) cc_final: 0.5388 (mtt180) REVERT: K 515 GLU cc_start: 0.5571 (mm-30) cc_final: 0.4973 (pm20) REVERT: K 649 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3537 (mm) outliers start: 57 outliers final: 33 residues processed: 1063 average time/residue: 0.5927 time to fit residues: 1016.1711 Evaluate side-chains 462 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 425 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain L residue 56 LYS Chi-restraints excluded: chain L residue 75 LYS Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain J residue 56 LYS Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain K residue 56 LYS Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 594 optimal weight: 20.0000 chunk 533 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 359 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 551 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 410 optimal weight: 2.9990 chunk 639 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 246 ASN A 263 HIS A 363 ASN A 409 ASN A 541 GLN B 263 HIS B 363 ASN B 409 ASN B 422 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 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN C 263 HIS C 363 ASN C 409 ASN C 541 GLN F 263 HIS F 363 ASN F 409 ASN F 422 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 769 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN D 263 HIS D 363 ASN D 409 ASN D 541 GLN G 263 HIS 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 769 GLN ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN E 263 HIS E 363 ASN E 409 ASN E 541 GLN H 263 HIS H 363 ASN H 409 ASN H 463 ASN H 697 ASN 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: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 57860 Z= 0.166 Angle : 0.554 7.442 78252 Z= 0.302 Chirality : 0.045 0.164 8852 Planarity : 0.005 0.042 10148 Dihedral : 5.684 50.764 7674 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.52 % Allowed : 7.23 % Favored : 91.25 % 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: -1.95 (0.09), residues: 6996 helix: -1.06 (0.10), residues: 2192 sheet: -0.50 (0.15), residues: 1192 loop : -1.70 (0.09), residues: 3612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 570 HIS 0.004 0.001 HIS A 211 PHE 0.016 0.002 PHE K 585 TYR 0.014 0.001 TYR G 699 ARG 0.006 0.001 ARG A 659 *********************** 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 643 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 546 time to evaluate : 5.149 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: A 221 SER cc_start: 0.8580 (p) cc_final: 0.8319 (m) REVERT: A 266 MET cc_start: 0.8212 (ttm) cc_final: 0.7945 (ttt) REVERT: A 350 MET cc_start: 0.7513 (mtp) cc_final: 0.7264 (mtp) REVERT: A 576 THR cc_start: 0.9074 (p) cc_final: 0.8842 (t) REVERT: A 587 MET cc_start: 0.8611 (mtt) cc_final: 0.8345 (mtt) REVERT: B 380 THR cc_start: 0.9133 (m) cc_final: 0.8476 (p) REVERT: B 453 ASP cc_start: 0.8134 (p0) cc_final: 0.7679 (p0) REVERT: B 587 MET cc_start: 0.8672 (mtt) cc_final: 0.8099 (mtt) REVERT: B 630 ASN cc_start: 0.5477 (t0) cc_final: 0.5037 (m-40) REVERT: B 662 MET cc_start: 0.6701 (mtm) cc_final: 0.6446 (mtm) REVERT: L 515 GLU cc_start: 0.5331 (mm-30) cc_final: 0.4668 (pm20) REVERT: L 589 ASN cc_start: 0.7202 (m-40) cc_final: 0.6728 (t0) REVERT: L 752 ARG cc_start: 0.6473 (ttt90) cc_final: 0.5566 (ptp-110) REVERT: C 221 SER cc_start: 0.8589 (p) cc_final: 0.8324 (m) REVERT: C 266 MET cc_start: 0.8211 (ttm) cc_final: 0.7940 (ttt) REVERT: C 350 MET cc_start: 0.7652 (mtp) cc_final: 0.7394 (mtp) REVERT: C 576 THR cc_start: 0.9074 (p) cc_final: 0.8845 (t) REVERT: C 587 MET cc_start: 0.8608 (mtt) cc_final: 0.8347 (mtt) REVERT: F 380 THR cc_start: 0.9097 (m) cc_final: 0.8461 (p) REVERT: F 453 ASP cc_start: 0.8191 (p0) cc_final: 0.7749 (p0) REVERT: F 587 MET cc_start: 0.8677 (mtt) cc_final: 0.8105 (mtt) REVERT: F 630 ASN cc_start: 0.5483 (t0) cc_final: 0.5043 (m-40) REVERT: F 662 MET cc_start: 0.6704 (mtm) cc_final: 0.6442 (mtm) REVERT: I 515 GLU cc_start: 0.5335 (mm-30) cc_final: 0.4672 (pm20) REVERT: I 589 ASN cc_start: 0.7205 (m-40) cc_final: 0.6731 (t0) REVERT: I 752 ARG cc_start: 0.6475 (ttt90) cc_final: 0.5568 (ptp-110) REVERT: D 221 SER cc_start: 0.8594 (p) cc_final: 0.8329 (m) REVERT: D 266 MET cc_start: 0.8213 (ttm) cc_final: 0.7942 (ttt) REVERT: D 350 MET cc_start: 0.7512 (mtp) cc_final: 0.7258 (mtp) REVERT: D 576 THR cc_start: 0.9072 (p) cc_final: 0.8843 (t) REVERT: D 587 MET cc_start: 0.8602 (mtt) cc_final: 0.8343 (mtt) REVERT: G 380 THR cc_start: 0.9093 (m) cc_final: 0.8462 (p) REVERT: G 453 ASP cc_start: 0.8181 (p0) cc_final: 0.7745 (p0) REVERT: G 587 MET cc_start: 0.8676 (mtt) cc_final: 0.8100 (mtt) REVERT: G 630 ASN cc_start: 0.5483 (t0) cc_final: 0.5041 (m-40) REVERT: G 662 MET cc_start: 0.6701 (mtm) cc_final: 0.6440 (mtm) REVERT: J 515 GLU cc_start: 0.5333 (mm-30) cc_final: 0.4669 (pm20) REVERT: J 589 ASN cc_start: 0.7207 (m-40) cc_final: 0.6733 (t0) REVERT: J 752 ARG cc_start: 0.6479 (ttt90) cc_final: 0.5640 (ptp-170) REVERT: E 221 SER cc_start: 0.8593 (p) cc_final: 0.8321 (m) REVERT: E 266 MET cc_start: 0.8213 (ttm) cc_final: 0.7946 (ttt) REVERT: E 350 MET cc_start: 0.7515 (mtp) cc_final: 0.7262 (mtp) REVERT: E 576 THR cc_start: 0.9068 (p) cc_final: 0.8835 (t) REVERT: E 587 MET cc_start: 0.8607 (mtt) cc_final: 0.8343 (mtt) REVERT: H 380 THR cc_start: 0.9093 (m) cc_final: 0.8462 (p) REVERT: H 453 ASP cc_start: 0.8186 (p0) cc_final: 0.7749 (p0) REVERT: H 587 MET cc_start: 0.8677 (mtt) cc_final: 0.8102 (mtt) REVERT: H 630 ASN cc_start: 0.5479 (t0) cc_final: 0.5040 (m-40) REVERT: H 662 MET cc_start: 0.6701 (mtm) cc_final: 0.6440 (mtm) REVERT: K 515 GLU cc_start: 0.5326 (mm-30) cc_final: 0.4662 (pm20) REVERT: K 589 ASN cc_start: 0.7203 (m-40) cc_final: 0.6729 (t0) REVERT: K 752 ARG cc_start: 0.6481 (ttt90) cc_final: 0.5645 (ptp-170) outliers start: 97 outliers final: 65 residues processed: 631 average time/residue: 0.5419 time to fit residues: 580.3830 Evaluate side-chains 481 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 416 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 355 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 532 optimal weight: 4.9990 chunk 435 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 640 optimal weight: 5.9990 chunk 691 optimal weight: 20.0000 chunk 570 optimal weight: 0.0570 chunk 635 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 513 optimal weight: 8.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- 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 463 ASN B 211 HIS L 32 GLN L 586 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN F 211 HIS I 32 GLN I 586 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN G 211 HIS J 32 GLN J 586 ASN ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN H 211 HIS K 586 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 57860 Z= 0.293 Angle : 0.591 7.191 78252 Z= 0.315 Chirality : 0.047 0.145 8852 Planarity : 0.004 0.049 10148 Dihedral : 5.447 52.750 7626 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.91 % Allowed : 7.79 % Favored : 89.30 % 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: -1.45 (0.09), residues: 6996 helix: -0.39 (0.11), residues: 2220 sheet: -0.39 (0.15), residues: 1192 loop : -1.52 (0.10), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 570 HIS 0.005 0.001 HIS J 280 PHE 0.016 0.002 PHE J 190 TYR 0.020 0.002 TYR B 732 ARG 0.005 0.001 ARG C 659 *********************** 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 614 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 428 time to evaluate : 5.090 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: A 266 MET cc_start: 0.8173 (ttm) cc_final: 0.7893 (ttt) REVERT: A 350 MET cc_start: 0.7608 (mtp) cc_final: 0.7352 (mtp) REVERT: A 455 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9068 (p) REVERT: A 576 THR cc_start: 0.9132 (p) cc_final: 0.8907 (t) REVERT: A 579 ASP cc_start: 0.8230 (p0) cc_final: 0.7948 (p0) REVERT: B 380 THR cc_start: 0.8996 (m) cc_final: 0.8347 (p) REVERT: B 453 ASP cc_start: 0.8073 (p0) cc_final: 0.7663 (p0) REVERT: B 501 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9125 (m) REVERT: B 587 MET cc_start: 0.8651 (mtt) cc_final: 0.8099 (mtt) REVERT: B 662 MET cc_start: 0.6787 (mtm) cc_final: 0.6526 (mtm) REVERT: L 219 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8670 (mttt) REVERT: L 515 GLU cc_start: 0.5671 (mm-30) cc_final: 0.4798 (pm20) REVERT: L 589 ASN cc_start: 0.7257 (m-40) cc_final: 0.6799 (t0) REVERT: L 639 ILE cc_start: 0.5683 (OUTLIER) cc_final: 0.5336 (mt) REVERT: L 695 TYR cc_start: 0.6266 (t80) cc_final: 0.6027 (t80) REVERT: L 752 ARG cc_start: 0.6381 (ttt90) cc_final: 0.5578 (ptp-110) REVERT: C 266 MET cc_start: 0.8164 (ttm) cc_final: 0.7882 (ttt) REVERT: C 350 MET cc_start: 0.7609 (mtp) cc_final: 0.7352 (mtp) REVERT: C 455 VAL cc_start: 0.9359 (OUTLIER) cc_final: 0.9069 (p) REVERT: C 576 THR cc_start: 0.9133 (p) cc_final: 0.8909 (t) REVERT: C 579 ASP cc_start: 0.8235 (p0) cc_final: 0.7949 (p0) REVERT: F 380 THR cc_start: 0.9021 (m) cc_final: 0.8352 (p) REVERT: F 453 ASP cc_start: 0.8173 (p0) cc_final: 0.7689 (p0) REVERT: F 587 MET cc_start: 0.8651 (mtt) cc_final: 0.8099 (mtt) REVERT: F 662 MET cc_start: 0.6786 (mtm) cc_final: 0.6524 (mtm) REVERT: I 219 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8671 (mttt) REVERT: I 515 GLU cc_start: 0.5669 (mm-30) cc_final: 0.4799 (pm20) REVERT: I 589 ASN cc_start: 0.7257 (m-40) cc_final: 0.6802 (t0) REVERT: I 639 ILE cc_start: 0.5683 (OUTLIER) cc_final: 0.5340 (mt) REVERT: I 695 TYR cc_start: 0.6261 (t80) cc_final: 0.6021 (t80) REVERT: I 752 ARG cc_start: 0.6384 (ttt90) cc_final: 0.5580 (ptp-110) REVERT: D 266 MET cc_start: 0.8173 (ttm) cc_final: 0.7892 (ttt) REVERT: D 350 MET cc_start: 0.7606 (mtp) cc_final: 0.7349 (mtp) REVERT: D 455 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9073 (p) REVERT: D 576 THR cc_start: 0.9132 (p) cc_final: 0.8907 (t) REVERT: D 579 ASP cc_start: 0.8233 (p0) cc_final: 0.7947 (p0) REVERT: G 380 THR cc_start: 0.9018 (m) cc_final: 0.8354 (p) REVERT: G 453 ASP cc_start: 0.8172 (p0) cc_final: 0.7689 (p0) REVERT: G 587 MET cc_start: 0.8655 (mtt) cc_final: 0.8096 (mtt) REVERT: G 662 MET cc_start: 0.6784 (mtm) cc_final: 0.6523 (mtm) REVERT: J 219 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8672 (mttt) REVERT: J 515 GLU cc_start: 0.5674 (mm-30) cc_final: 0.4797 (pm20) REVERT: J 589 ASN cc_start: 0.7259 (m-40) cc_final: 0.6806 (t0) REVERT: J 639 ILE cc_start: 0.5687 (OUTLIER) cc_final: 0.5343 (mt) REVERT: J 695 TYR cc_start: 0.6263 (t80) cc_final: 0.6019 (t80) REVERT: J 752 ARG cc_start: 0.6391 (ttt90) cc_final: 0.5584 (ptp-110) REVERT: E 266 MET cc_start: 0.8170 (ttm) cc_final: 0.7892 (ttt) REVERT: E 350 MET cc_start: 0.7606 (mtp) cc_final: 0.7344 (mtp) REVERT: E 455 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9073 (p) REVERT: E 576 THR cc_start: 0.9130 (p) cc_final: 0.8904 (t) REVERT: E 579 ASP cc_start: 0.8229 (p0) cc_final: 0.7948 (p0) REVERT: H 380 THR cc_start: 0.9015 (m) cc_final: 0.8353 (p) REVERT: H 453 ASP cc_start: 0.8175 (p0) cc_final: 0.7692 (p0) REVERT: H 587 MET cc_start: 0.8654 (mtt) cc_final: 0.8097 (mtt) REVERT: H 662 MET cc_start: 0.6780 (mtm) cc_final: 0.6520 (mtm) REVERT: K 219 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8671 (mttt) REVERT: K 515 GLU cc_start: 0.5666 (mm-30) cc_final: 0.4792 (pm20) REVERT: K 589 ASN cc_start: 0.7252 (m-40) cc_final: 0.6800 (t0) REVERT: K 639 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5337 (mt) REVERT: K 695 TYR cc_start: 0.6264 (t80) cc_final: 0.6022 (t80) REVERT: K 752 ARG cc_start: 0.6392 (ttt90) cc_final: 0.5588 (ptp-110) outliers start: 186 outliers final: 97 residues processed: 590 average time/residue: 0.5117 time to fit residues: 519.8459 Evaluate side-chains 481 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 371 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 219 LYS Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 639 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 724 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 219 LYS Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 639 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 455 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain E residue 707 ILE Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 639 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 632 optimal weight: 2.9990 chunk 481 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 305 optimal weight: 20.0000 chunk 430 optimal weight: 4.9990 chunk 642 optimal weight: 8.9990 chunk 680 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 609 optimal weight: 2.9990 chunk 183 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 57860 Z= 0.189 Angle : 0.515 6.931 78252 Z= 0.275 Chirality : 0.044 0.166 8852 Planarity : 0.004 0.044 10148 Dihedral : 5.066 51.791 7626 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.50 % Allowed : 9.79 % Favored : 87.70 % 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: -0.97 (0.10), residues: 6996 helix: 0.10 (0.11), residues: 2188 sheet: -0.22 (0.15), residues: 1220 loop : -1.25 (0.10), residues: 3588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 570 HIS 0.004 0.001 HIS K 197 PHE 0.013 0.001 PHE A 202 TYR 0.016 0.001 TYR E 694 ARG 0.008 0.000 ARG K 590 *********************** 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 591 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 431 time to evaluate : 5.204 Fit side-chains REVERT: A 221 SER cc_start: 0.8766 (p) cc_final: 0.8404 (m) REVERT: A 266 MET cc_start: 0.8156 (ttm) cc_final: 0.7872 (ttt) REVERT: A 350 MET cc_start: 0.7693 (mtp) cc_final: 0.7380 (mtp) REVERT: A 576 THR cc_start: 0.9090 (p) cc_final: 0.8885 (t) REVERT: A 579 ASP cc_start: 0.8161 (p0) cc_final: 0.7939 (p0) REVERT: B 453 ASP cc_start: 0.8062 (p0) cc_final: 0.7853 (p0) REVERT: B 579 ASP cc_start: 0.7828 (p0) cc_final: 0.7612 (p0) REVERT: B 587 MET cc_start: 0.8672 (mtt) cc_final: 0.8442 (mtt) REVERT: B 662 MET cc_start: 0.6807 (mtm) cc_final: 0.6537 (mtm) REVERT: L 285 LEU cc_start: 0.4597 (tp) cc_final: 0.4395 (tp) REVERT: L 412 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.2100 (m-80) REVERT: L 515 GLU cc_start: 0.5720 (mm-30) cc_final: 0.4782 (pm20) REVERT: L 589 ASN cc_start: 0.7131 (m-40) cc_final: 0.6779 (t0) REVERT: L 639 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5179 (mt) REVERT: L 649 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3192 (mp) REVERT: L 695 TYR cc_start: 0.6222 (t80) cc_final: 0.5962 (t80) REVERT: L 752 ARG cc_start: 0.6480 (ttt90) cc_final: 0.5694 (ptp-110) REVERT: C 221 SER cc_start: 0.8779 (p) cc_final: 0.8413 (m) REVERT: C 266 MET cc_start: 0.8150 (ttm) cc_final: 0.7868 (ttt) REVERT: C 350 MET cc_start: 0.7696 (mtp) cc_final: 0.7372 (mtp) REVERT: C 576 THR cc_start: 0.9092 (p) cc_final: 0.8884 (t) REVERT: C 579 ASP cc_start: 0.8165 (p0) cc_final: 0.7941 (p0) REVERT: F 380 THR cc_start: 0.9033 (m) cc_final: 0.8416 (p) REVERT: F 453 ASP cc_start: 0.8135 (p0) cc_final: 0.7835 (p0) REVERT: F 579 ASP cc_start: 0.7830 (p0) cc_final: 0.7608 (p0) REVERT: F 587 MET cc_start: 0.8669 (mtt) cc_final: 0.8439 (mtt) REVERT: F 662 MET cc_start: 0.6805 (mtm) cc_final: 0.6565 (mtm) REVERT: I 285 LEU cc_start: 0.4590 (tp) cc_final: 0.4387 (tp) REVERT: I 412 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.2099 (m-80) REVERT: I 515 GLU cc_start: 0.5724 (mm-30) cc_final: 0.4783 (pm20) REVERT: I 589 ASN cc_start: 0.7132 (m-40) cc_final: 0.6779 (t0) REVERT: I 639 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.5181 (mt) REVERT: I 649 ILE cc_start: 0.3747 (OUTLIER) cc_final: 0.3189 (mp) REVERT: I 695 TYR cc_start: 0.6216 (t80) cc_final: 0.5959 (t80) REVERT: I 752 ARG cc_start: 0.6487 (ttt90) cc_final: 0.5701 (ptp-110) REVERT: D 221 SER cc_start: 0.8784 (p) cc_final: 0.8416 (m) REVERT: D 266 MET cc_start: 0.8159 (ttm) cc_final: 0.7873 (ttt) REVERT: D 350 MET cc_start: 0.7690 (mtp) cc_final: 0.7375 (mtp) REVERT: D 576 THR cc_start: 0.9091 (p) cc_final: 0.8883 (t) REVERT: D 579 ASP cc_start: 0.8166 (p0) cc_final: 0.7938 (p0) REVERT: G 380 THR cc_start: 0.9028 (m) cc_final: 0.8417 (p) REVERT: G 453 ASP cc_start: 0.8126 (p0) cc_final: 0.7831 (p0) REVERT: G 579 ASP cc_start: 0.7833 (p0) cc_final: 0.7614 (p0) REVERT: G 587 MET cc_start: 0.8674 (mtt) cc_final: 0.8437 (mtt) REVERT: G 662 MET cc_start: 0.6811 (mtm) cc_final: 0.6572 (mtm) REVERT: J 285 LEU cc_start: 0.4600 (tp) cc_final: 0.4398 (tp) REVERT: J 412 TYR cc_start: 0.3570 (OUTLIER) cc_final: 0.2102 (m-80) REVERT: J 515 GLU cc_start: 0.5725 (mm-30) cc_final: 0.4785 (pm20) REVERT: J 589 ASN cc_start: 0.7131 (m-40) cc_final: 0.6779 (t0) REVERT: J 639 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5182 (mt) REVERT: J 649 ILE cc_start: 0.3750 (OUTLIER) cc_final: 0.3190 (mp) REVERT: J 695 TYR cc_start: 0.6219 (t80) cc_final: 0.5957 (t80) REVERT: J 752 ARG cc_start: 0.6425 (ttt90) cc_final: 0.5643 (ptp-170) REVERT: E 221 SER cc_start: 0.8772 (p) cc_final: 0.8413 (m) REVERT: E 266 MET cc_start: 0.8160 (ttm) cc_final: 0.7873 (ttt) REVERT: E 350 MET cc_start: 0.7691 (mtp) cc_final: 0.7374 (mtp) REVERT: E 576 THR cc_start: 0.9087 (p) cc_final: 0.8879 (t) REVERT: E 579 ASP cc_start: 0.8162 (p0) cc_final: 0.7936 (p0) REVERT: H 380 THR cc_start: 0.9027 (m) cc_final: 0.8416 (p) REVERT: H 453 ASP cc_start: 0.8128 (p0) cc_final: 0.7830 (p0) REVERT: H 579 ASP cc_start: 0.7837 (p0) cc_final: 0.7616 (p0) REVERT: H 587 MET cc_start: 0.8672 (mtt) cc_final: 0.8441 (mtt) REVERT: H 662 MET cc_start: 0.6803 (mtm) cc_final: 0.6565 (mtm) REVERT: K 285 LEU cc_start: 0.4600 (tp) cc_final: 0.4396 (tp) REVERT: K 412 TYR cc_start: 0.3572 (OUTLIER) cc_final: 0.2106 (m-80) REVERT: K 515 GLU cc_start: 0.5718 (mm-30) cc_final: 0.4779 (pm20) REVERT: K 589 ASN cc_start: 0.7130 (m-40) cc_final: 0.6777 (t0) REVERT: K 639 ILE cc_start: 0.5567 (OUTLIER) cc_final: 0.5183 (mt) REVERT: K 649 ILE cc_start: 0.3748 (OUTLIER) cc_final: 0.3190 (mp) REVERT: K 695 TYR cc_start: 0.6218 (t80) cc_final: 0.5957 (t80) REVERT: K 752 ARG cc_start: 0.6421 (ttt90) cc_final: 0.5641 (ptp-170) outliers start: 160 outliers final: 106 residues processed: 567 average time/residue: 0.5002 time to fit residues: 495.7083 Evaluate side-chains 492 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 374 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 412 TYR Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 639 ILE Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 412 TYR Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 639 ILE Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 412 TYR Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 639 ILE Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 412 TYR Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 639 ILE Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 566 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 506 optimal weight: 0.0270 chunk 280 optimal weight: 6.9990 chunk 580 optimal weight: 7.9990 chunk 470 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 347 optimal weight: 1.9990 chunk 610 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 563 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 563 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 563 GLN ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 57860 Z= 0.190 Angle : 0.508 6.654 78252 Z= 0.272 Chirality : 0.044 0.156 8852 Planarity : 0.003 0.044 10148 Dihedral : 4.907 52.086 7626 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.64 % Allowed : 10.12 % Favored : 87.23 % 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: -0.70 (0.10), residues: 6996 helix: 0.37 (0.11), residues: 2192 sheet: -0.09 (0.15), residues: 1244 loop : -1.12 (0.10), residues: 3560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 570 HIS 0.004 0.001 HIS L 280 PHE 0.016 0.001 PHE B 493 TYR 0.016 0.001 TYR A 694 ARG 0.007 0.000 ARG D 659 *********************** 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 583 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 414 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.8861 (p) cc_final: 0.8477 (m) REVERT: A 266 MET cc_start: 0.8157 (ttm) cc_final: 0.7876 (ttt) REVERT: A 350 MET cc_start: 0.7721 (mtp) cc_final: 0.7382 (mtp) REVERT: A 576 THR cc_start: 0.9082 (p) cc_final: 0.8873 (t) REVERT: A 579 ASP cc_start: 0.8159 (p0) cc_final: 0.7941 (p0) REVERT: B 662 MET cc_start: 0.6773 (mtm) cc_final: 0.6535 (mtm) REVERT: L 335 LYS cc_start: 0.4925 (mmtp) cc_final: 0.4037 (ttpt) REVERT: L 515 GLU cc_start: 0.5575 (mm-30) cc_final: 0.4778 (pm20) REVERT: L 531 ASP cc_start: 0.8001 (p0) cc_final: 0.7753 (p0) REVERT: L 589 ASN cc_start: 0.7182 (m-40) cc_final: 0.6785 (t0) REVERT: L 649 ILE cc_start: 0.3741 (OUTLIER) cc_final: 0.3148 (mp) REVERT: L 679 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6522 (m-40) REVERT: L 695 TYR cc_start: 0.6172 (t80) cc_final: 0.5882 (t80) REVERT: C 221 SER cc_start: 0.8871 (p) cc_final: 0.8485 (m) REVERT: C 266 MET cc_start: 0.8152 (ttm) cc_final: 0.7871 (ttt) REVERT: C 350 MET cc_start: 0.7723 (mtp) cc_final: 0.7377 (mtp) REVERT: C 576 THR cc_start: 0.9083 (p) cc_final: 0.8873 (t) REVERT: C 579 ASP cc_start: 0.8164 (p0) cc_final: 0.7943 (p0) REVERT: F 380 THR cc_start: 0.9023 (m) cc_final: 0.8438 (p) REVERT: F 453 ASP cc_start: 0.8162 (p0) cc_final: 0.7908 (p0) REVERT: F 455 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8830 (t) REVERT: F 662 MET cc_start: 0.6791 (mtm) cc_final: 0.6519 (mtm) REVERT: I 335 LYS cc_start: 0.4888 (mmtp) cc_final: 0.4050 (ttpt) REVERT: I 515 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4780 (pm20) REVERT: I 531 ASP cc_start: 0.8009 (p0) cc_final: 0.7758 (p0) REVERT: I 589 ASN cc_start: 0.7183 (m-40) cc_final: 0.6786 (t0) REVERT: I 649 ILE cc_start: 0.3741 (OUTLIER) cc_final: 0.3149 (mp) REVERT: I 679 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6522 (m-40) REVERT: I 695 TYR cc_start: 0.6175 (t80) cc_final: 0.5881 (t80) REVERT: D 221 SER cc_start: 0.8877 (p) cc_final: 0.8486 (m) REVERT: D 266 MET cc_start: 0.8162 (ttm) cc_final: 0.7876 (ttt) REVERT: D 350 MET cc_start: 0.7721 (mtp) cc_final: 0.7376 (mtp) REVERT: D 576 THR cc_start: 0.9083 (p) cc_final: 0.8874 (t) REVERT: D 579 ASP cc_start: 0.8164 (p0) cc_final: 0.7944 (p0) REVERT: G 380 THR cc_start: 0.9018 (m) cc_final: 0.8438 (p) REVERT: G 453 ASP cc_start: 0.8157 (p0) cc_final: 0.7902 (p0) REVERT: G 455 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8832 (t) REVERT: G 662 MET cc_start: 0.6792 (mtm) cc_final: 0.6519 (mtm) REVERT: J 335 LYS cc_start: 0.4890 (mmtp) cc_final: 0.4054 (ttpt) REVERT: J 515 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4780 (pm20) REVERT: J 531 ASP cc_start: 0.8014 (p0) cc_final: 0.7762 (p0) REVERT: J 589 ASN cc_start: 0.7179 (m-40) cc_final: 0.6788 (t0) REVERT: J 649 ILE cc_start: 0.3744 (OUTLIER) cc_final: 0.3150 (mp) REVERT: J 679 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6526 (m-40) REVERT: J 695 TYR cc_start: 0.6174 (t80) cc_final: 0.5880 (t80) REVERT: J 752 ARG cc_start: 0.6423 (ttt90) cc_final: 0.5692 (ptp-170) REVERT: E 221 SER cc_start: 0.8848 (p) cc_final: 0.8454 (m) REVERT: E 266 MET cc_start: 0.8164 (ttm) cc_final: 0.7879 (ttt) REVERT: E 350 MET cc_start: 0.7718 (mtp) cc_final: 0.7372 (mtp) REVERT: E 576 THR cc_start: 0.9081 (p) cc_final: 0.8871 (t) REVERT: E 579 ASP cc_start: 0.8155 (p0) cc_final: 0.7941 (p0) REVERT: H 380 THR cc_start: 0.9018 (m) cc_final: 0.8435 (p) REVERT: H 453 ASP cc_start: 0.8156 (p0) cc_final: 0.7903 (p0) REVERT: H 455 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8818 (t) REVERT: H 662 MET cc_start: 0.6788 (mtm) cc_final: 0.6515 (mtm) REVERT: K 335 LYS cc_start: 0.4931 (mmtp) cc_final: 0.4041 (ttpt) REVERT: K 515 GLU cc_start: 0.5570 (mm-30) cc_final: 0.4772 (pm20) REVERT: K 531 ASP cc_start: 0.8002 (p0) cc_final: 0.7755 (p0) REVERT: K 589 ASN cc_start: 0.7181 (m-40) cc_final: 0.6787 (t0) REVERT: K 649 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3143 (mp) REVERT: K 679 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6526 (m-40) REVERT: K 695 TYR cc_start: 0.6177 (t80) cc_final: 0.5885 (t80) REVERT: K 752 ARG cc_start: 0.6422 (ttt90) cc_final: 0.5694 (ptp-170) outliers start: 169 outliers final: 123 residues processed: 559 average time/residue: 0.5156 time to fit residues: 498.5849 Evaluate side-chains 485 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 351 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 228 optimal weight: 10.0000 chunk 612 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 399 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 chunk 565 optimal weight: 5.9990 chunk 315 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 357 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 57860 Z= 0.268 Angle : 0.551 6.829 78252 Z= 0.294 Chirality : 0.046 0.196 8852 Planarity : 0.004 0.043 10148 Dihedral : 5.053 51.857 7626 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.80 % Allowed : 10.06 % Favored : 87.14 % 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: -0.73 (0.10), residues: 6996 helix: 0.33 (0.11), residues: 2192 sheet: -0.07 (0.15), residues: 1176 loop : -1.12 (0.10), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 570 HIS 0.005 0.001 HIS J 280 PHE 0.019 0.002 PHE B 493 TYR 0.018 0.002 TYR H 732 ARG 0.004 0.000 ARG A 659 *********************** 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 559 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 380 time to evaluate : 6.539 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8210 (ttm) cc_final: 0.7965 (ttt) REVERT: A 350 MET cc_start: 0.7736 (mtp) cc_final: 0.7440 (mtp) REVERT: A 480 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8632 (m) REVERT: A 576 THR cc_start: 0.9090 (p) cc_final: 0.8803 (t) REVERT: B 535 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7316 (pp20) REVERT: B 662 MET cc_start: 0.6799 (mtm) cc_final: 0.6378 (mtm) REVERT: L 335 LYS cc_start: 0.5075 (mmtp) cc_final: 0.4245 (ttpt) REVERT: L 515 GLU cc_start: 0.5647 (mm-30) cc_final: 0.4809 (pm20) REVERT: L 589 ASN cc_start: 0.7366 (m-40) cc_final: 0.6948 (t0) REVERT: L 649 ILE cc_start: 0.3589 (OUTLIER) cc_final: 0.2996 (mp) REVERT: L 678 ARG cc_start: 0.6621 (ptm160) cc_final: 0.6068 (ptm-80) REVERT: L 695 TYR cc_start: 0.6242 (t80) cc_final: 0.5982 (t80) REVERT: L 752 ARG cc_start: 0.5864 (ptm160) cc_final: 0.5393 (ptp-170) REVERT: C 266 MET cc_start: 0.8200 (ttm) cc_final: 0.7957 (ttt) REVERT: C 350 MET cc_start: 0.7736 (mtp) cc_final: 0.7431 (mtp) REVERT: C 480 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8634 (m) REVERT: C 576 THR cc_start: 0.9091 (p) cc_final: 0.8800 (t) REVERT: F 380 THR cc_start: 0.8932 (m) cc_final: 0.8161 (p) REVERT: F 453 ASP cc_start: 0.8148 (p0) cc_final: 0.7791 (p0) REVERT: F 455 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8832 (m) REVERT: F 535 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7321 (pp20) REVERT: F 662 MET cc_start: 0.6786 (mtm) cc_final: 0.6367 (mtm) REVERT: I 335 LYS cc_start: 0.5080 (mmtp) cc_final: 0.4250 (ttpt) REVERT: I 515 GLU cc_start: 0.5651 (mm-30) cc_final: 0.4806 (pm20) REVERT: I 589 ASN cc_start: 0.7373 (m-40) cc_final: 0.6949 (t0) REVERT: I 649 ILE cc_start: 0.3594 (OUTLIER) cc_final: 0.3000 (mp) REVERT: I 678 ARG cc_start: 0.6623 (ptm160) cc_final: 0.6068 (ptm-80) REVERT: I 695 TYR cc_start: 0.6243 (t80) cc_final: 0.5981 (t80) REVERT: I 752 ARG cc_start: 0.5865 (ptm160) cc_final: 0.5390 (ptp-170) REVERT: D 266 MET cc_start: 0.8203 (ttm) cc_final: 0.7960 (ttt) REVERT: D 350 MET cc_start: 0.7733 (mtp) cc_final: 0.7434 (mtp) REVERT: D 480 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (m) REVERT: D 576 THR cc_start: 0.9092 (p) cc_final: 0.8803 (t) REVERT: G 380 THR cc_start: 0.8928 (m) cc_final: 0.8163 (p) REVERT: G 453 ASP cc_start: 0.8142 (p0) cc_final: 0.7786 (p0) REVERT: G 455 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (m) REVERT: G 535 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7319 (pp20) REVERT: G 662 MET cc_start: 0.6787 (mtm) cc_final: 0.6367 (mtm) REVERT: J 335 LYS cc_start: 0.5084 (mmtp) cc_final: 0.4255 (ttpt) REVERT: J 515 GLU cc_start: 0.5647 (mm-30) cc_final: 0.4808 (pm20) REVERT: J 589 ASN cc_start: 0.7367 (m-40) cc_final: 0.6952 (t0) REVERT: J 649 ILE cc_start: 0.3593 (OUTLIER) cc_final: 0.2999 (mp) REVERT: J 678 ARG cc_start: 0.6622 (ptm160) cc_final: 0.6074 (ptm-80) REVERT: J 695 TYR cc_start: 0.6243 (t80) cc_final: 0.5981 (t80) REVERT: J 752 ARG cc_start: 0.6374 (ttt90) cc_final: 0.5633 (ptp-110) REVERT: E 266 MET cc_start: 0.8209 (ttm) cc_final: 0.7963 (ttt) REVERT: E 350 MET cc_start: 0.7729 (mtp) cc_final: 0.7430 (mtp) REVERT: E 480 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8624 (m) REVERT: E 576 THR cc_start: 0.9088 (p) cc_final: 0.8799 (t) REVERT: E 724 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7790 (tp) REVERT: H 380 THR cc_start: 0.8926 (m) cc_final: 0.8154 (p) REVERT: H 453 ASP cc_start: 0.8143 (p0) cc_final: 0.7786 (p0) REVERT: H 455 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8831 (m) REVERT: H 535 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: H 662 MET cc_start: 0.6776 (mtm) cc_final: 0.6359 (mtm) REVERT: K 335 LYS cc_start: 0.5081 (mmtp) cc_final: 0.4251 (ttpt) REVERT: K 515 GLU cc_start: 0.5644 (mm-30) cc_final: 0.4805 (pm20) REVERT: K 589 ASN cc_start: 0.7366 (m-40) cc_final: 0.6948 (t0) REVERT: K 649 ILE cc_start: 0.3590 (OUTLIER) cc_final: 0.2999 (mp) REVERT: K 678 ARG cc_start: 0.6620 (ptm160) cc_final: 0.6071 (ptm-80) REVERT: K 695 TYR cc_start: 0.6245 (t80) cc_final: 0.5984 (t80) REVERT: K 752 ARG cc_start: 0.6373 (ttt90) cc_final: 0.5635 (ptp-110) outliers start: 179 outliers final: 138 residues processed: 538 average time/residue: 0.5056 time to fit residues: 476.5777 Evaluate side-chains 499 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 345 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 535 GLU Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 628 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 434 MET Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 535 GLU Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 656 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 497 optimal weight: 0.8980 chunk 385 optimal weight: 6.9990 chunk 573 optimal weight: 0.0470 chunk 380 optimal weight: 5.9990 chunk 678 optimal weight: 7.9990 chunk 424 optimal weight: 0.0060 chunk 413 optimal weight: 3.9990 chunk 313 optimal weight: 20.0000 overall best weight: 1.5898 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 57860 Z= 0.163 Angle : 0.492 6.569 78252 Z= 0.264 Chirality : 0.045 0.296 8852 Planarity : 0.003 0.043 10148 Dihedral : 4.747 51.110 7626 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.53 % Allowed : 10.33 % Favored : 87.14 % 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: -0.45 (0.10), residues: 6996 helix: 0.58 (0.11), residues: 2192 sheet: 0.09 (0.15), residues: 1184 loop : -0.96 (0.10), residues: 3620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 570 HIS 0.003 0.001 HIS K 197 PHE 0.015 0.001 PHE D 202 TYR 0.017 0.001 TYR A 694 ARG 0.003 0.000 ARG C 659 *********************** 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 560 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 398 time to evaluate : 5.236 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.8891 (p) cc_final: 0.8486 (m) REVERT: A 350 MET cc_start: 0.7761 (mtp) cc_final: 0.7405 (mtp) REVERT: A 576 THR cc_start: 0.9072 (p) cc_final: 0.8802 (t) REVERT: A 724 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7574 (tp) REVERT: B 535 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7294 (pp20) REVERT: B 662 MET cc_start: 0.6743 (mtm) cc_final: 0.6525 (mtm) REVERT: B 673 LYS cc_start: 0.6489 (mtpt) cc_final: 0.6147 (mmtt) REVERT: L 39 ILE cc_start: 0.9109 (tp) cc_final: 0.8756 (tp) REVERT: L 335 LYS cc_start: 0.4936 (mmtp) cc_final: 0.4251 (ttpt) REVERT: L 515 GLU cc_start: 0.5580 (mm-30) cc_final: 0.4701 (pm20) REVERT: L 589 ASN cc_start: 0.7280 (m-40) cc_final: 0.6811 (t0) REVERT: L 649 ILE cc_start: 0.3718 (OUTLIER) cc_final: 0.3104 (mp) REVERT: L 678 ARG cc_start: 0.6472 (ptm160) cc_final: 0.5927 (ptm-80) REVERT: L 744 MET cc_start: 0.6655 (mmm) cc_final: 0.6150 (ttt) REVERT: C 221 SER cc_start: 0.8903 (p) cc_final: 0.8493 (m) REVERT: C 350 MET cc_start: 0.7759 (mtp) cc_final: 0.7409 (mtp) REVERT: C 576 THR cc_start: 0.9069 (p) cc_final: 0.8798 (t) REVERT: C 724 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7575 (tp) REVERT: F 380 THR cc_start: 0.9047 (m) cc_final: 0.8581 (p) REVERT: F 455 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8810 (t) REVERT: F 535 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: F 662 MET cc_start: 0.6725 (mtm) cc_final: 0.6506 (mtm) REVERT: F 673 LYS cc_start: 0.6491 (mtpt) cc_final: 0.6150 (mmtt) REVERT: I 39 ILE cc_start: 0.9113 (tp) cc_final: 0.8758 (tp) REVERT: I 335 LYS cc_start: 0.4943 (mmtp) cc_final: 0.4256 (ttpt) REVERT: I 515 GLU cc_start: 0.5587 (mm-30) cc_final: 0.4704 (pm20) REVERT: I 589 ASN cc_start: 0.7282 (m-40) cc_final: 0.6810 (t0) REVERT: I 649 ILE cc_start: 0.3715 (OUTLIER) cc_final: 0.3106 (mp) REVERT: I 678 ARG cc_start: 0.6470 (ptm160) cc_final: 0.5929 (ptm-80) REVERT: I 744 MET cc_start: 0.6656 (mmm) cc_final: 0.6149 (ttt) REVERT: D 221 SER cc_start: 0.8908 (p) cc_final: 0.8495 (m) REVERT: D 350 MET cc_start: 0.7760 (mtp) cc_final: 0.7404 (mtp) REVERT: D 576 THR cc_start: 0.9072 (p) cc_final: 0.8799 (t) REVERT: D 724 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7576 (tp) REVERT: G 380 THR cc_start: 0.9042 (m) cc_final: 0.8582 (p) REVERT: G 455 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8817 (t) REVERT: G 535 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7300 (pp20) REVERT: G 662 MET cc_start: 0.6728 (mtm) cc_final: 0.6508 (mtm) REVERT: G 673 LYS cc_start: 0.6493 (mtpt) cc_final: 0.6151 (mmtt) REVERT: J 39 ILE cc_start: 0.9117 (tp) cc_final: 0.8764 (tp) REVERT: J 335 LYS cc_start: 0.4947 (mmtp) cc_final: 0.4261 (ttpt) REVERT: J 515 GLU cc_start: 0.5581 (mm-30) cc_final: 0.4701 (pm20) REVERT: J 589 ASN cc_start: 0.7282 (m-40) cc_final: 0.6815 (t0) REVERT: J 649 ILE cc_start: 0.3716 (OUTLIER) cc_final: 0.3108 (mp) REVERT: J 678 ARG cc_start: 0.6476 (ptm160) cc_final: 0.5936 (ptm-80) REVERT: J 752 ARG cc_start: 0.6379 (ttt90) cc_final: 0.5641 (ptp-110) REVERT: E 221 SER cc_start: 0.8896 (p) cc_final: 0.8489 (m) REVERT: E 350 MET cc_start: 0.7759 (mtp) cc_final: 0.7401 (mtp) REVERT: E 576 THR cc_start: 0.9066 (p) cc_final: 0.8797 (t) REVERT: E 724 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7580 (tp) REVERT: H 380 THR cc_start: 0.9038 (m) cc_final: 0.8576 (p) REVERT: H 455 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (t) REVERT: H 535 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7295 (pp20) REVERT: H 662 MET cc_start: 0.6724 (mtm) cc_final: 0.6505 (mtm) REVERT: H 673 LYS cc_start: 0.6493 (mtpt) cc_final: 0.6150 (mmtt) REVERT: K 39 ILE cc_start: 0.9115 (tp) cc_final: 0.8761 (tp) REVERT: K 335 LYS cc_start: 0.4945 (mmtp) cc_final: 0.4258 (ttpt) REVERT: K 515 GLU cc_start: 0.5576 (mm-30) cc_final: 0.4697 (pm20) REVERT: K 589 ASN cc_start: 0.7279 (m-40) cc_final: 0.6813 (t0) REVERT: K 649 ILE cc_start: 0.3710 (OUTLIER) cc_final: 0.3100 (mp) REVERT: K 678 ARG cc_start: 0.6477 (ptm160) cc_final: 0.5932 (ptm-80) REVERT: K 752 ARG cc_start: 0.6379 (ttt90) cc_final: 0.5641 (ptp-110) outliers start: 162 outliers final: 117 residues processed: 547 average time/residue: 0.4929 time to fit residues: 472.9637 Evaluate side-chains 487 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 355 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 455 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 535 GLU Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 724 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 455 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 628 LEU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain E residue 724 ILE Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 535 GLU Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 419 optimal weight: 9.9990 chunk 270 optimal weight: 0.9980 chunk 405 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 131 optimal weight: 30.0000 chunk 431 optimal weight: 3.9990 chunk 462 optimal weight: 9.9990 chunk 335 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 533 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 211 ASN ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 211 ASN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 654 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN J 211 ASN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 654 HIS ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 ASN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 654 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 57860 Z= 0.354 Angle : 0.603 7.445 78252 Z= 0.322 Chirality : 0.049 0.351 8852 Planarity : 0.004 0.042 10148 Dihedral : 5.279 52.028 7626 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.07 % Allowed : 10.64 % Favored : 86.30 % 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: -0.77 (0.10), residues: 6996 helix: 0.37 (0.11), residues: 2168 sheet: -0.21 (0.15), residues: 1200 loop : -1.15 (0.10), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 570 HIS 0.008 0.001 HIS J 280 PHE 0.018 0.002 PHE J 190 TYR 0.025 0.002 TYR I 600 ARG 0.003 0.000 ARG A 659 *********************** 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 577 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 381 time to evaluate : 5.209 Fit side-chains revert: symmetry clash REVERT: A 350 MET cc_start: 0.7767 (mtp) cc_final: 0.7488 (mtp) REVERT: A 576 THR cc_start: 0.9105 (p) cc_final: 0.8786 (t) REVERT: B 662 MET cc_start: 0.6758 (mtm) cc_final: 0.6553 (mtm) REVERT: L 335 LYS cc_start: 0.5080 (mmtp) cc_final: 0.4320 (ttpt) REVERT: L 515 GLU cc_start: 0.5844 (mm-30) cc_final: 0.4574 (pm20) REVERT: L 589 ASN cc_start: 0.7399 (m-40) cc_final: 0.7015 (t0) REVERT: L 649 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.2969 (mp) REVERT: L 678 ARG cc_start: 0.6597 (ptm160) cc_final: 0.6026 (ptm-80) REVERT: L 695 TYR cc_start: 0.6273 (t80) cc_final: 0.6002 (t80) REVERT: L 744 MET cc_start: 0.6654 (mmm) cc_final: 0.6179 (ttt) REVERT: C 350 MET cc_start: 0.7767 (mtp) cc_final: 0.7487 (mtp) REVERT: C 576 THR cc_start: 0.9103 (p) cc_final: 0.8781 (t) REVERT: F 380 THR cc_start: 0.8956 (m) cc_final: 0.8673 (p) REVERT: F 662 MET cc_start: 0.6777 (mtm) cc_final: 0.6559 (mtm) REVERT: I 335 LYS cc_start: 0.5086 (mmtp) cc_final: 0.4322 (ttpt) REVERT: I 515 GLU cc_start: 0.5846 (mm-30) cc_final: 0.4576 (pm20) REVERT: I 589 ASN cc_start: 0.7400 (m-40) cc_final: 0.7015 (t0) REVERT: I 649 ILE cc_start: 0.3558 (OUTLIER) cc_final: 0.2970 (mp) REVERT: I 678 ARG cc_start: 0.6597 (ptm160) cc_final: 0.6026 (ptm-80) REVERT: I 695 TYR cc_start: 0.6276 (t80) cc_final: 0.6001 (t80) REVERT: I 744 MET cc_start: 0.6656 (mmm) cc_final: 0.6180 (ttt) REVERT: D 350 MET cc_start: 0.7765 (mtp) cc_final: 0.7482 (mtp) REVERT: D 576 THR cc_start: 0.9104 (p) cc_final: 0.8783 (t) REVERT: G 380 THR cc_start: 0.8954 (m) cc_final: 0.8679 (p) REVERT: G 662 MET cc_start: 0.6781 (mtm) cc_final: 0.6562 (mtm) REVERT: J 335 LYS cc_start: 0.5092 (mmtp) cc_final: 0.4331 (ttpt) REVERT: J 515 GLU cc_start: 0.5845 (mm-30) cc_final: 0.4576 (pm20) REVERT: J 589 ASN cc_start: 0.7397 (m-40) cc_final: 0.7018 (t0) REVERT: J 649 ILE cc_start: 0.3563 (OUTLIER) cc_final: 0.2975 (mp) REVERT: J 678 ARG cc_start: 0.6601 (ptm160) cc_final: 0.6038 (ptm-80) REVERT: J 695 TYR cc_start: 0.6277 (t80) cc_final: 0.6010 (t80) REVERT: J 744 MET cc_start: 0.6502 (mmm) cc_final: 0.6249 (ttt) REVERT: J 752 ARG cc_start: 0.6283 (ttt90) cc_final: 0.5708 (ptp-110) REVERT: E 350 MET cc_start: 0.7765 (mtp) cc_final: 0.7484 (mtp) REVERT: E 576 THR cc_start: 0.9101 (p) cc_final: 0.8779 (t) REVERT: H 380 THR cc_start: 0.8947 (m) cc_final: 0.8671 (p) REVERT: H 662 MET cc_start: 0.6776 (mtm) cc_final: 0.6555 (mtm) REVERT: K 335 LYS cc_start: 0.5088 (mmtp) cc_final: 0.4327 (ttpt) REVERT: K 515 GLU cc_start: 0.5843 (mm-30) cc_final: 0.4571 (pm20) REVERT: K 589 ASN cc_start: 0.7395 (m-40) cc_final: 0.7016 (t0) REVERT: K 649 ILE cc_start: 0.3556 (OUTLIER) cc_final: 0.2968 (mp) REVERT: K 678 ARG cc_start: 0.6603 (ptm160) cc_final: 0.6038 (ptm-80) REVERT: K 695 TYR cc_start: 0.6277 (t80) cc_final: 0.6013 (t80) REVERT: K 744 MET cc_start: 0.6506 (mmm) cc_final: 0.6253 (ttt) REVERT: K 752 ARG cc_start: 0.6285 (ttt90) cc_final: 0.5710 (ptp-110) outliers start: 196 outliers final: 145 residues processed: 561 average time/residue: 0.5005 time to fit residues: 489.5423 Evaluate side-chains 499 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 350 time to evaluate : 5.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 40 MET Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 296 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 701 VAL Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 701 VAL Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 40 MET Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 240 THR Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 701 VAL Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 40 MET Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 617 optimal weight: 3.9990 chunk 650 optimal weight: 2.9990 chunk 593 optimal weight: 4.9990 chunk 632 optimal weight: 4.9990 chunk 649 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 275 optimal weight: 0.5980 chunk 496 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 571 optimal weight: 0.9980 chunk 598 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 57860 Z= 0.144 Angle : 0.495 6.689 78252 Z= 0.265 Chirality : 0.044 0.288 8852 Planarity : 0.003 0.041 10148 Dihedral : 4.752 51.882 7626 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.25 % Allowed : 11.33 % Favored : 86.42 % 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: -0.43 (0.10), residues: 6996 helix: 0.60 (0.11), residues: 2192 sheet: -0.01 (0.15), residues: 1168 loop : -0.91 (0.10), residues: 3636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 570 HIS 0.003 0.001 HIS K 197 PHE 0.016 0.001 PHE B 493 TYR 0.018 0.001 TYR C 694 ARG 0.003 0.000 ARG D 659 *********************** 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 516 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 372 time to evaluate : 5.189 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.8913 (p) cc_final: 0.8513 (m) REVERT: A 350 MET cc_start: 0.7668 (mtp) cc_final: 0.7309 (mtp) REVERT: A 576 THR cc_start: 0.8989 (p) cc_final: 0.8759 (t) REVERT: B 662 MET cc_start: 0.6703 (mtm) cc_final: 0.6498 (mtm) REVERT: L 39 ILE cc_start: 0.9156 (tp) cc_final: 0.8761 (tp) REVERT: L 335 LYS cc_start: 0.4955 (mmtp) cc_final: 0.4364 (ttpt) REVERT: L 515 GLU cc_start: 0.5662 (mm-30) cc_final: 0.4652 (pm20) REVERT: L 589 ASN cc_start: 0.7267 (m-40) cc_final: 0.6872 (t0) REVERT: L 649 ILE cc_start: 0.3706 (OUTLIER) cc_final: 0.3092 (mp) REVERT: L 678 ARG cc_start: 0.6285 (ptm160) cc_final: 0.5778 (ptm-80) REVERT: L 744 MET cc_start: 0.6712 (mmm) cc_final: 0.5952 (ttt) REVERT: C 221 SER cc_start: 0.8921 (p) cc_final: 0.8526 (m) REVERT: C 350 MET cc_start: 0.7666 (mtp) cc_final: 0.7312 (mtp) REVERT: C 576 THR cc_start: 0.8986 (p) cc_final: 0.8753 (t) REVERT: F 662 MET cc_start: 0.6685 (mtm) cc_final: 0.6475 (mtm) REVERT: I 39 ILE cc_start: 0.9158 (tp) cc_final: 0.8761 (tp) REVERT: I 335 LYS cc_start: 0.4958 (mmtp) cc_final: 0.4364 (ttpt) REVERT: I 515 GLU cc_start: 0.5666 (mm-30) cc_final: 0.4656 (pm20) REVERT: I 589 ASN cc_start: 0.7272 (m-40) cc_final: 0.6871 (t0) REVERT: I 649 ILE cc_start: 0.3708 (OUTLIER) cc_final: 0.3089 (mp) REVERT: I 678 ARG cc_start: 0.6285 (ptm160) cc_final: 0.5778 (ptm-80) REVERT: I 744 MET cc_start: 0.6718 (mmm) cc_final: 0.5958 (ttt) REVERT: D 221 SER cc_start: 0.8926 (p) cc_final: 0.8525 (m) REVERT: D 350 MET cc_start: 0.7664 (mtp) cc_final: 0.7307 (mtp) REVERT: D 576 THR cc_start: 0.8988 (p) cc_final: 0.8755 (t) REVERT: G 587 MET cc_start: 0.8681 (mtt) cc_final: 0.8479 (mmm) REVERT: G 662 MET cc_start: 0.6687 (mtm) cc_final: 0.6470 (mtm) REVERT: J 39 ILE cc_start: 0.9161 (tp) cc_final: 0.8766 (tp) REVERT: J 335 LYS cc_start: 0.4962 (mmtp) cc_final: 0.4369 (ttpt) REVERT: J 515 GLU cc_start: 0.5661 (mm-30) cc_final: 0.4653 (pm20) REVERT: J 589 ASN cc_start: 0.7267 (m-40) cc_final: 0.6874 (t0) REVERT: J 649 ILE cc_start: 0.3705 (OUTLIER) cc_final: 0.3088 (mp) REVERT: J 678 ARG cc_start: 0.6296 (ptm160) cc_final: 0.5788 (ptm-80) REVERT: J 744 MET cc_start: 0.6558 (mmm) cc_final: 0.5984 (ttt) REVERT: J 752 ARG cc_start: 0.6177 (ttt90) cc_final: 0.5622 (ptp-110) REVERT: E 221 SER cc_start: 0.8913 (p) cc_final: 0.8517 (m) REVERT: E 350 MET cc_start: 0.7670 (mtp) cc_final: 0.7308 (mtp) REVERT: E 576 THR cc_start: 0.8985 (p) cc_final: 0.8751 (t) REVERT: H 662 MET cc_start: 0.6680 (mtm) cc_final: 0.6465 (mtm) REVERT: K 39 ILE cc_start: 0.9163 (tp) cc_final: 0.8770 (tp) REVERT: K 335 LYS cc_start: 0.4964 (mmtp) cc_final: 0.4371 (ttpt) REVERT: K 515 GLU cc_start: 0.5658 (mm-30) cc_final: 0.4648 (pm20) REVERT: K 589 ASN cc_start: 0.7266 (m-40) cc_final: 0.6872 (t0) REVERT: K 649 ILE cc_start: 0.3698 (OUTLIER) cc_final: 0.3081 (mp) REVERT: K 678 ARG cc_start: 0.6299 (ptm160) cc_final: 0.5792 (ptm-80) REVERT: K 744 MET cc_start: 0.6559 (mmm) cc_final: 0.5984 (ttt) REVERT: K 752 ARG cc_start: 0.6179 (ttt90) cc_final: 0.5624 (ptp-110) outliers start: 144 outliers final: 119 residues processed: 497 average time/residue: 0.5077 time to fit residues: 443.7676 Evaluate side-chains 477 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 354 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 683 ASP Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain F residue 683 ASP Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 683 ASP Chi-restraints excluded: chain G residue 726 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 612 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain H residue 683 ASP Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 630 optimal weight: 1.9990 chunk 415 optimal weight: 20.0000 chunk 668 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 317 optimal weight: 20.0000 chunk 464 optimal weight: 0.0010 chunk 701 optimal weight: 8.9990 chunk 645 optimal weight: 0.0670 chunk 558 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 overall best weight: 0.9728 ------------------------------------------------------------------------------- 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** B 463 ASN B 709 ASN L 563 GLN ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 ASN F 709 ASN I 563 GLN ** I 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN G 709 ASN ** J 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 463 ASN H 709 ASN ** K 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3912 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= 0.134 Angle : 0.481 6.739 78252 Z= 0.256 Chirality : 0.044 0.155 8852 Planarity : 0.003 0.042 10148 Dihedral : 4.489 50.364 7626 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.75 % Allowed : 11.75 % Favored : 86.50 % 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: -0.04 (0.10), residues: 6996 helix: 0.96 (0.12), residues: 2152 sheet: 0.14 (0.15), residues: 1240 loop : -0.66 (0.10), residues: 3604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 570 HIS 0.003 0.001 HIS H 263 PHE 0.015 0.001 PHE B 493 TYR 0.018 0.001 TYR E 694 ARG 0.004 0.000 ARG D 659 ********************** 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 525 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 413 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.8862 (p) cc_final: 0.8488 (m) REVERT: A 350 MET cc_start: 0.7711 (mtp) cc_final: 0.7341 (mtp) REVERT: A 576 THR cc_start: 0.8908 (p) cc_final: 0.8694 (t) REVERT: B 472 ASP cc_start: 0.8656 (t70) cc_final: 0.8358 (t0) REVERT: B 662 MET cc_start: 0.6619 (mtm) cc_final: 0.6410 (mtm) REVERT: L 39 ILE cc_start: 0.9187 (tp) cc_final: 0.8788 (tp) REVERT: L 335 LYS cc_start: 0.4922 (mmtp) cc_final: 0.4337 (ttpt) REVERT: L 416 ILE cc_start: 0.7218 (mt) cc_final: 0.7015 (tt) REVERT: L 515 GLU cc_start: 0.5404 (mm-30) cc_final: 0.4579 (pm20) REVERT: L 589 ASN cc_start: 0.7213 (m-40) cc_final: 0.6795 (t0) REVERT: L 600 TYR cc_start: 0.6525 (m-80) cc_final: 0.6286 (m-80) REVERT: L 649 ILE cc_start: 0.3586 (OUTLIER) cc_final: 0.2982 (mp) REVERT: L 678 ARG cc_start: 0.6222 (ptm160) cc_final: 0.5641 (ptm-80) REVERT: L 679 ASN cc_start: 0.6970 (OUTLIER) cc_final: 0.6429 (m-40) REVERT: L 721 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6087 (pt0) REVERT: L 744 MET cc_start: 0.6769 (mmm) cc_final: 0.5940 (ttt) REVERT: C 221 SER cc_start: 0.8868 (p) cc_final: 0.8490 (m) REVERT: C 350 MET cc_start: 0.7711 (mtp) cc_final: 0.7344 (mtp) REVERT: C 576 THR cc_start: 0.8904 (p) cc_final: 0.8693 (t) REVERT: F 472 ASP cc_start: 0.8671 (t70) cc_final: 0.8369 (t0) REVERT: F 662 MET cc_start: 0.6608 (mtm) cc_final: 0.6405 (mtm) REVERT: I 39 ILE cc_start: 0.9187 (tp) cc_final: 0.8784 (tp) REVERT: I 335 LYS cc_start: 0.4919 (mmtp) cc_final: 0.4334 (ttpt) REVERT: I 416 ILE cc_start: 0.7218 (mt) cc_final: 0.7013 (tt) REVERT: I 515 GLU cc_start: 0.5399 (mm-30) cc_final: 0.4584 (pm20) REVERT: I 589 ASN cc_start: 0.7210 (m-40) cc_final: 0.6790 (t0) REVERT: I 600 TYR cc_start: 0.6522 (m-80) cc_final: 0.6287 (m-80) REVERT: I 649 ILE cc_start: 0.3581 (OUTLIER) cc_final: 0.2979 (mp) REVERT: I 678 ARG cc_start: 0.6223 (ptm160) cc_final: 0.5641 (ptm-80) REVERT: I 679 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6433 (m-40) REVERT: I 721 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6088 (pt0) REVERT: I 744 MET cc_start: 0.6774 (mmm) cc_final: 0.5940 (ttt) REVERT: D 221 SER cc_start: 0.8875 (p) cc_final: 0.8492 (m) REVERT: D 350 MET cc_start: 0.7708 (mtp) cc_final: 0.7336 (mtp) REVERT: D 576 THR cc_start: 0.8909 (p) cc_final: 0.8695 (t) REVERT: G 472 ASP cc_start: 0.8671 (t70) cc_final: 0.8377 (t0) REVERT: G 662 MET cc_start: 0.6611 (mtm) cc_final: 0.6401 (mtm) REVERT: J 39 ILE cc_start: 0.9190 (tp) cc_final: 0.8789 (tp) REVERT: J 335 LYS cc_start: 0.4926 (mmtp) cc_final: 0.4339 (ttpt) REVERT: J 416 ILE cc_start: 0.7224 (mt) cc_final: 0.7018 (tt) REVERT: J 515 GLU cc_start: 0.5399 (mm-30) cc_final: 0.4580 (pm20) REVERT: J 589 ASN cc_start: 0.7210 (m-40) cc_final: 0.6795 (t0) REVERT: J 600 TYR cc_start: 0.6522 (m-80) cc_final: 0.6287 (m-80) REVERT: J 649 ILE cc_start: 0.3577 (OUTLIER) cc_final: 0.2976 (mp) REVERT: J 678 ARG cc_start: 0.6238 (ptm160) cc_final: 0.5648 (ptm-80) REVERT: J 679 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6433 (m-40) REVERT: J 721 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6111 (pt0) REVERT: J 744 MET cc_start: 0.6647 (mmm) cc_final: 0.5931 (ttt) REVERT: J 752 ARG cc_start: 0.6194 (ttt90) cc_final: 0.5597 (ptp-110) REVERT: E 221 SER cc_start: 0.8862 (p) cc_final: 0.8489 (m) REVERT: E 350 MET cc_start: 0.7707 (mtp) cc_final: 0.7338 (mtp) REVERT: E 576 THR cc_start: 0.8903 (p) cc_final: 0.8690 (t) REVERT: H 472 ASP cc_start: 0.8674 (t70) cc_final: 0.8381 (t0) REVERT: H 662 MET cc_start: 0.6606 (mtm) cc_final: 0.6398 (mtm) REVERT: K 39 ILE cc_start: 0.9194 (tp) cc_final: 0.8802 (tp) REVERT: K 335 LYS cc_start: 0.4923 (mmtp) cc_final: 0.4339 (ttpt) REVERT: K 416 ILE cc_start: 0.7224 (mt) cc_final: 0.7020 (tt) REVERT: K 515 GLU cc_start: 0.5397 (mm-30) cc_final: 0.4578 (pm20) REVERT: K 589 ASN cc_start: 0.7214 (m-40) cc_final: 0.6797 (t0) REVERT: K 600 TYR cc_start: 0.6523 (m-80) cc_final: 0.6286 (m-80) REVERT: K 649 ILE cc_start: 0.3565 (OUTLIER) cc_final: 0.2966 (mp) REVERT: K 678 ARG cc_start: 0.6235 (ptm160) cc_final: 0.5646 (ptm-80) REVERT: K 679 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6434 (m-40) REVERT: K 721 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6115 (pt0) REVERT: K 744 MET cc_start: 0.6648 (mmm) cc_final: 0.5935 (ttt) REVERT: K 752 ARG cc_start: 0.6192 (ttt90) cc_final: 0.5597 (ptp-110) outliers start: 112 outliers final: 99 residues processed: 517 average time/residue: 0.5106 time to fit residues: 459.5902 Evaluate side-chains 472 residues out of total 6412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 365 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 154 ILE Chi-restraints excluded: chain L residue 159 ILE Chi-restraints excluded: chain L residue 233 LEU Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 435 ILE Chi-restraints excluded: chain L residue 532 VAL Chi-restraints excluded: chain L residue 550 VAL Chi-restraints excluded: chain L residue 615 ILE Chi-restraints excluded: chain L residue 632 THR Chi-restraints excluded: chain L residue 649 ILE Chi-restraints excluded: chain L residue 658 LEU Chi-restraints excluded: chain L residue 679 ASN Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 616 HIS Chi-restraints excluded: chain F residue 644 VAL Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 532 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 615 ILE Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 649 ILE Chi-restraints excluded: chain I residue 658 LEU Chi-restraints excluded: chain I residue 679 ASN Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 616 HIS Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain J residue 159 ILE Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 435 ILE Chi-restraints excluded: chain J residue 532 VAL Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 615 ILE Chi-restraints excluded: chain J residue 632 THR Chi-restraints excluded: chain J residue 649 ILE Chi-restraints excluded: chain J residue 658 LEU Chi-restraints excluded: chain J residue 679 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 668 LEU Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 367 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 616 HIS Chi-restraints excluded: chain H residue 644 VAL Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 154 ILE Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 532 VAL Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain K residue 615 ILE Chi-restraints excluded: chain K residue 632 THR Chi-restraints excluded: chain K residue 649 ILE Chi-restraints excluded: chain K residue 658 LEU Chi-restraints excluded: chain K residue 679 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 342 optimal weight: 0.9990 chunk 443 optimal weight: 0.0270 chunk 594 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 514 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 155 optimal weight: 8.9990 chunk 559 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 574 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 1.4644 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.160736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128024 restraints weight = 91978.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121072 restraints weight = 87814.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.122130 restraints weight = 127114.090| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3973 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= 0.157 Angle : 0.487 8.519 78252 Z= 0.259 Chirality : 0.044 0.147 8852 Planarity : 0.003 0.041 10148 Dihedral : 4.509 49.412 7624 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 12.08 % Favored : 85.97 % 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: -0.04 (0.10), residues: 6996 helix: 0.91 (0.12), residues: 2176 sheet: 0.24 (0.15), residues: 1240 loop : -0.68 (0.10), residues: 3580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 271 HIS 0.003 0.001 HIS K 197 PHE 0.016 0.001 PHE C 675 TYR 0.022 0.001 TYR C 681 ARG 0.002 0.000 ARG D 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9751.08 seconds wall clock time: 173 minutes 55.45 seconds (10435.45 seconds total)