Starting phenix.real_space_refine on Sun Apr 14 10:44:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b41_15836/04_2024/8b41_15836.pdb" } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 155 5.16 5 C 20336 2.51 5 N 5217 2.21 5 O 5551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "E TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31259 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "B" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5922 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 27, 'TRANS': 690} Chain breaks: 2 Chain: "D" Number of atoms: 6030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 6030 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2125 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 5, 'TRANS': 248} Chain breaks: 3 Chain: "F" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1618 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain breaks: 2 Chain: "G" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "I" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "J" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 903 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Time building chain proxies: 15.86, per 1000 atoms: 0.51 Number of scatterers: 31259 At special positions: 0 Unit cell: (180.978, 128.898, 207.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 155 16.00 O 5551 8.00 N 5217 7.00 C 20336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.65 Conformation dependent library (CDL) restraints added in 6.0 seconds 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 29 sheets defined 50.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.741A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.606A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.529A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.099A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.835A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 286 removed outlier: 3.866A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 344 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.541A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 4.179A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.592A pdb=" N VAL A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 444 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 445' Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.858A pdb=" N ALA A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.414A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.501A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.611A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.653A pdb=" N GLY A 705 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.725A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.921A pdb=" N GLY A 751 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 removed outlier: 3.728A pdb=" N CYS A 776 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.959A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 141 Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.759A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.658A pdb=" N SER B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 4.018A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY B 222 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 286 removed outlier: 4.205A pdb=" N THR B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.887A pdb=" N THR B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.750A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.720A pdb=" N ILE B 379 " --> pdb=" O MET B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.218A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.624A pdb=" N ASN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 535 through 543 removed outlier: 4.047A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 586 through 590 removed outlier: 4.048A pdb=" N LYS B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 590 " --> pdb=" O LEU B 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 590' Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.744A pdb=" N ILE B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.543A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.593A pdb=" N GLY B 705 " --> pdb=" O ALA B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.729A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 751 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 776 removed outlier: 3.658A pdb=" N CYS B 776 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 795 through 807 Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.600A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 removed outlier: 3.800A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 124 through 141 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.163A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 176 removed outlier: 3.876A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 removed outlier: 4.210A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.913A pdb=" N THR C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 removed outlier: 3.829A pdb=" N LEU C 328 " --> pdb=" O PHE C 324 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS C 336 " --> pdb=" O TYR C 332 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.561A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.509A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.621A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 441 through 445 removed outlier: 4.083A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.663A pdb=" N LEU C 515 " --> pdb=" O ILE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 543 removed outlier: 3.908A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 542 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.614A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.043A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 679 through 684 removed outlier: 3.523A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.800A pdb=" N GLY C 705 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 707 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 729 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.683A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 751 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 776 removed outlier: 3.628A pdb=" N CYS C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 808 Processing helix chain 'D' and resid 16 through 20 removed outlier: 4.141A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.907A pdb=" N THR D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 141 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.762A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.053A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.860A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.767A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.981A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 384 through 392 removed outlier: 3.854A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE D 390 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 409 Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 439 through 445 removed outlier: 3.806A pdb=" N LEU D 445 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.747A pdb=" N GLU D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.623A pdb=" N ARG D 541 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 566 Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.582A pdb=" N ILE D 610 " --> pdb=" O PRO D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.635A pdb=" N ILE D 633 " --> pdb=" O GLU D 630 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 636 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 678 through 684 Processing helix chain 'D' and resid 701 through 707 removed outlier: 3.551A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 705 " --> pdb=" O ALA D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.964A pdb=" N CYS D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 753 removed outlier: 4.102A pdb=" N GLY D 751 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 776 removed outlier: 3.557A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 795 through 808 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.773A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 121 through 148 Proline residue: E 128 - end of helix removed outlier: 4.026A pdb=" N TRP E 145 " --> pdb=" O CYS E 141 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 168 removed outlier: 3.887A pdb=" N SER E 168 " --> pdb=" O LYS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 252 removed outlier: 3.545A pdb=" N LEU E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 284 removed outlier: 4.375A pdb=" N ALA E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 312 through 342 removed outlier: 3.690A pdb=" N LYS E 318 " --> pdb=" O HIS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 381 removed outlier: 3.760A pdb=" N ILE E 377 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 removed outlier: 3.593A pdb=" N ARG E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU E 392 " --> pdb=" O PHE E 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.909A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.535A pdb=" N LYS F 125 " --> pdb=" O HIS F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 148 removed outlier: 4.461A pdb=" N TRP F 145 " --> pdb=" O CYS F 141 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.693A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 285 removed outlier: 3.723A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 343 removed outlier: 3.796A pdb=" N PHE F 321 " --> pdb=" O SER F 317 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS F 322 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR F 337 " --> pdb=" O THR F 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.819A pdb=" N HIS G 32 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR G 91 " --> pdb=" O PRO G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.664A pdb=" N ARG H 31 " --> pdb=" O PRO H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.534A pdb=" N ARG J 31 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.412A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 619 " --> pdb=" O LYS A 645 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 713 " --> pdb=" O HIS A 737 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 459 through 461 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 421 through 422 removed outlier: 6.397A pdb=" N LEU B 521 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS B 552 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 523 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 549 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN B 575 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 551 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 619 " --> pdb=" O LYS B 645 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU B 667 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AA8, first strand: chain 'B' and resid 735 through 737 removed outlier: 6.698A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 759 " --> pdb=" O VAL B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 421 through 422 removed outlier: 4.153A pdb=" N THR C 421 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 428 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU C 498 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR C 524 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 500 " --> pdb=" O THR C 524 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 521 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LYS C 552 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 523 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 619 " --> pdb=" O LYS C 645 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 691 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 713 " --> pdb=" O HIS C 737 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.253A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 421 through 422 removed outlier: 6.340A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR D 477 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU D 453 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 498 " --> pdb=" O HIS D 522 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR D 524 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 500 " --> pdb=" O THR D 524 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU D 549 " --> pdb=" O SER D 573 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASN D 575 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 551 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 596 " --> pdb=" O GLU D 618 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 460 through 461 Processing sheet with id=AB5, first strand: chain 'D' and resid 643 through 645 removed outlier: 7.057A pdb=" N LEU D 644 " --> pdb=" O TYR D 668 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU D 713 " --> pdb=" O HIS D 737 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 759 through 760 removed outlier: 6.716A pdb=" N ILE D 759 " --> pdb=" O VAL D 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB9, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.883A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 13 Processing sheet with id=AC3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.545A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.734A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.347A pdb=" N GLY J 10 " --> pdb=" O THR J 112 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.347A pdb=" N GLY J 10 " --> pdb=" O THR J 112 " (cutoff:3.500A) 1504 hydrogen bonds defined for protein. 3882 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: 12.53 Time building geometry restraints manager: 13.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9795 1.34 - 1.46: 7535 1.46 - 1.58: 14443 1.58 - 1.70: 0 1.70 - 1.81: 219 Bond restraints: 31992 Sorted by residual: bond pdb=" CA VAL J 100 " pdb=" CB VAL J 100 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 8.17e-01 bond pdb=" CA ASP E 256 " pdb=" CB ASP E 256 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.72e-01 bond pdb=" CA VAL I 100 " pdb=" CB VAL I 100 " ideal model delta sigma weight residual 1.531 1.540 -0.009 1.11e-02 8.12e+03 6.52e-01 bond pdb=" C LEU B 700 " pdb=" O LEU B 700 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.44e-01 bond pdb=" C ILE C 365 " pdb=" O ILE C 365 " ideal model delta sigma weight residual 1.232 1.239 -0.008 1.01e-02 9.80e+03 5.82e-01 ... (remaining 31987 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.95: 788 106.95 - 113.79: 18096 113.79 - 120.64: 13216 120.64 - 127.49: 10902 127.49 - 134.34: 346 Bond angle restraints: 43348 Sorted by residual: angle pdb=" C GLY E 255 " pdb=" N ASP E 256 " pdb=" CA ASP E 256 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" N LYS C 547 " pdb=" CA LYS C 547 " pdb=" C LYS C 547 " ideal model delta sigma weight residual 114.04 110.41 3.63 1.24e+00 6.50e-01 8.55e+00 angle pdb=" N GLN B 617 " pdb=" CA GLN B 617 " pdb=" C GLN B 617 " ideal model delta sigma weight residual 114.56 111.49 3.07 1.27e+00 6.20e-01 5.86e+00 angle pdb=" N LYS F 304 " pdb=" CA LYS F 304 " pdb=" C LYS F 304 " ideal model delta sigma weight residual 114.56 111.68 2.88 1.27e+00 6.20e-01 5.14e+00 angle pdb=" N VAL A 567 " pdb=" CA VAL A 567 " pdb=" C VAL A 567 " ideal model delta sigma weight residual 112.98 110.20 2.78 1.25e+00 6.40e-01 4.94e+00 ... (remaining 43343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 17692 16.72 - 33.43: 1169 33.43 - 50.15: 255 50.15 - 66.87: 47 66.87 - 83.59: 10 Dihedral angle restraints: 19173 sinusoidal: 7894 harmonic: 11279 Sorted by residual: dihedral pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" N ILE A 279 " pdb=" CA ILE A 279 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP D 458 " pdb=" CB ASP D 458 " pdb=" CG ASP D 458 " pdb=" OD1 ASP D 458 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA HIS D 253 " pdb=" C HIS D 253 " pdb=" N VAL D 254 " pdb=" CA VAL D 254 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 19170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2819 0.029 - 0.057: 1467 0.057 - 0.086: 395 0.086 - 0.114: 185 0.114 - 0.143: 37 Chirality restraints: 4903 Sorted by residual: chirality pdb=" CA VAL B 786 " pdb=" N VAL B 786 " pdb=" C VAL B 786 " pdb=" CB VAL B 786 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 654 " pdb=" N ILE A 654 " pdb=" C ILE A 654 " pdb=" CB ILE A 654 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE B 508 " pdb=" N ILE B 508 " pdb=" C ILE B 508 " pdb=" CB ILE B 508 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.56e-01 ... (remaining 4900 not shown) Planarity restraints: 5371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 320 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C ILE C 320 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE C 320 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 321 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 383 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO C 384 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 323 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C SER C 323 " 0.027 2.00e-02 2.50e+03 pdb=" O SER C 323 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE C 324 " -0.009 2.00e-02 2.50e+03 ... (remaining 5368 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1022 2.71 - 3.26: 32059 3.26 - 3.81: 51306 3.81 - 4.35: 64126 4.35 - 4.90: 106493 Nonbonded interactions: 255006 Sorted by model distance: nonbonded pdb=" OH TYR C 513 " pdb=" O VAL C 536 " model vdw 2.169 2.440 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.173 2.440 nonbonded pdb=" OG1 THR C 679 " pdb=" OD2 ASP C 703 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR D 48 " pdb=" OE1 GLN D 49 " model vdw 2.223 2.440 nonbonded pdb=" NH1 ARG A 419 " pdb=" O HIS A 431 " model vdw 2.228 2.520 ... (remaining 255001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 176 or resid 230 through 808)) selection = chain 'C' selection = (chain 'D' and (resid 15 through 176 or resid 230 through 808)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.520 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 83.040 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.002 0.030 31992 Z= 0.157 Angle : 0.482 7.151 43348 Z= 0.272 Chirality : 0.039 0.143 4903 Planarity : 0.003 0.040 5371 Dihedral : 11.826 83.587 11817 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.69 % Allowed : 7.60 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3759 helix: 0.13 (0.13), residues: 1674 sheet: -0.45 (0.21), residues: 626 loop : -0.60 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 24 HIS 0.004 0.001 HIS D 104 PHE 0.013 0.001 PHE C 250 TYR 0.013 0.001 TYR F 279 ARG 0.002 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 610 time to evaluate : 4.712 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 104 HIS cc_start: 0.9024 (OUTLIER) cc_final: 0.8506 (t70) REVERT: A 154 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: A 161 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8338 (pp) REVERT: A 236 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: A 238 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 410 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: A 426 ASP cc_start: 0.7072 (t0) cc_final: 0.6796 (t0) REVERT: A 546 LEU cc_start: 0.8267 (tp) cc_final: 0.7917 (tp) REVERT: A 583 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7181 (t) REVERT: A 597 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7575 (mp0) REVERT: A 613 LEU cc_start: 0.9053 (mt) cc_final: 0.8828 (tp) REVERT: A 664 LEU cc_start: 0.8972 (mt) cc_final: 0.8529 (mp) REVERT: A 687 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 769 LEU cc_start: 0.8413 (mt) cc_final: 0.8128 (tp) REVERT: B 226 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6692 (mmm-85) REVERT: B 326 ILE cc_start: 0.8819 (pt) cc_final: 0.8540 (mt) REVERT: B 444 ASP cc_start: 0.7953 (m-30) cc_final: 0.7650 (t0) REVERT: B 506 LYS cc_start: 0.8421 (pttm) cc_final: 0.8116 (tmtt) REVERT: B 570 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7926 (pp30) REVERT: B 806 ASP cc_start: 0.5733 (t70) cc_final: 0.5495 (t70) REVERT: C 52 MET cc_start: 0.8450 (mtp) cc_final: 0.8032 (mtm) REVERT: C 161 LEU cc_start: 0.7901 (mm) cc_final: 0.7686 (mt) REVERT: C 243 LEU cc_start: 0.8945 (tp) cc_final: 0.8724 (tp) REVERT: C 332 TYR cc_start: 0.8037 (t80) cc_final: 0.7722 (t80) REVERT: C 348 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7930 (mp) REVERT: C 355 SER cc_start: 0.7332 (t) cc_final: 0.6797 (m) REVERT: C 405 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7509 (mm) REVERT: C 422 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6748 (mmmm) REVERT: C 429 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5964 (pm20) REVERT: C 477 TYR cc_start: 0.8266 (m-10) cc_final: 0.8030 (m-10) REVERT: C 597 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7902 (mp0) REVERT: C 623 ASP cc_start: 0.8347 (t0) cc_final: 0.8081 (t0) REVERT: C 635 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6952 (m-10) REVERT: C 688 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7070 (mtp-110) REVERT: D 37 MET cc_start: 0.7448 (ttm) cc_final: 0.7214 (mtp) REVERT: D 115 GLU cc_start: 0.7959 (tp30) cc_final: 0.7643 (tp30) REVERT: D 135 ILE cc_start: 0.8834 (tt) cc_final: 0.8478 (mt) REVERT: D 173 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7939 (mt) REVERT: D 218 ARG cc_start: 0.7393 (ttt180) cc_final: 0.7110 (tmt170) REVERT: D 235 LYS cc_start: 0.7781 (mttt) cc_final: 0.7565 (ptpt) REVERT: D 297 VAL cc_start: 0.8854 (m) cc_final: 0.8621 (p) REVERT: D 353 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7008 (t80) REVERT: D 422 LYS cc_start: 0.7378 (mtpt) cc_final: 0.7119 (mmtt) REVERT: D 446 VAL cc_start: 0.7669 (m) cc_final: 0.6802 (p) REVERT: D 454 GLU cc_start: 0.7272 (tt0) cc_final: 0.6932 (tp30) REVERT: D 467 GLN cc_start: 0.7128 (mt0) cc_final: 0.6653 (tm-30) REVERT: D 545 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7564 (mtp85) REVERT: D 555 LEU cc_start: 0.7433 (mt) cc_final: 0.6882 (mp) REVERT: D 571 LYS cc_start: 0.8869 (tttm) cc_final: 0.8587 (ttpt) REVERT: D 587 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8147 (pp) REVERT: D 686 LYS cc_start: 0.7372 (mttp) cc_final: 0.6777 (mmmm) REVERT: E 46 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: E 99 LEU cc_start: 0.8904 (tp) cc_final: 0.8695 (tp) REVERT: E 261 MET cc_start: 0.4585 (tpp) cc_final: 0.4111 (tmm) REVERT: E 279 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7206 (p90) REVERT: E 348 GLU cc_start: 0.6716 (mt-10) cc_final: 0.5636 (pm20) REVERT: E 373 MET cc_start: 0.6802 (mtp) cc_final: 0.6538 (ttm) REVERT: E 379 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6845 (mm-40) REVERT: F 37 MET cc_start: 0.7937 (ttp) cc_final: 0.7666 (tpp) REVERT: F 44 THR cc_start: 0.8711 (m) cc_final: 0.8324 (p) REVERT: F 114 MET cc_start: 0.8564 (mmm) cc_final: 0.8224 (mmm) REVERT: F 156 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4427 (tm-30) REVERT: F 297 ILE cc_start: 0.9298 (pt) cc_final: 0.9089 (pt) REVERT: F 334 CYS cc_start: 0.5454 (OUTLIER) cc_final: 0.4894 (t) REVERT: G 46 GLU cc_start: 0.8679 (tt0) cc_final: 0.8289 (tp30) REVERT: G 56 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7853 (mp0) REVERT: G 104 TYR cc_start: 0.7988 (m-80) cc_final: 0.7444 (m-80) REVERT: H 13 GLN cc_start: 0.6879 (mp10) cc_final: 0.6491 (pm20) REVERT: H 87 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7608 (mmtm) REVERT: I 36 TRP cc_start: 0.5739 (m100) cc_final: 0.5386 (m100) REVERT: I 45 ARG cc_start: 0.5555 (ttm110) cc_final: 0.4851 (ttp-110) REVERT: I 74 ASN cc_start: 0.6022 (m-40) cc_final: 0.5238 (p0) REVERT: I 76 LYS cc_start: 0.7851 (mttm) cc_final: 0.7567 (mptt) REVERT: J 36 TRP cc_start: 0.6167 (m100) cc_final: 0.5177 (m100) outliers start: 163 outliers final: 69 residues processed: 751 average time/residue: 0.4592 time to fit residues: 540.6687 Evaluate side-chains 444 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 356 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 294 ASN Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 2.9990 chunk 284 optimal weight: 0.0270 chunk 158 optimal weight: 0.0570 chunk 97 optimal weight: 0.0470 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 294 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 0.0980 chunk 219 optimal weight: 0.6980 chunk 341 optimal weight: 2.9990 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN B 116 ASN B 406 ASN B 570 GLN B 592 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN C 408 ASN C 431 HIS D 418 GLN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN E 46 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN ** F 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS H 74 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.103 31992 Z= 0.153 Angle : 0.529 9.515 43348 Z= 0.278 Chirality : 0.040 0.199 4903 Planarity : 0.004 0.035 5371 Dihedral : 7.088 74.600 4343 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.35 % Allowed : 12.67 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3759 helix: 0.35 (0.13), residues: 1693 sheet: -0.29 (0.21), residues: 620 loop : -0.58 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 145 HIS 0.009 0.001 HIS J 32 PHE 0.022 0.001 PHE B 250 TYR 0.021 0.001 TYR D 325 ARG 0.007 0.000 ARG J 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 425 time to evaluate : 3.657 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: A 104 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8357 (t70) REVERT: A 154 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: A 161 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 238 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 402 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8245 (tm) REVERT: A 426 ASP cc_start: 0.7231 (t0) cc_final: 0.6929 (t0) REVERT: A 546 LEU cc_start: 0.8354 (tp) cc_final: 0.8049 (tp) REVERT: A 593 LEU cc_start: 0.8655 (tt) cc_final: 0.8353 (tt) REVERT: A 597 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7637 (mp0) REVERT: A 613 LEU cc_start: 0.9004 (mt) cc_final: 0.8803 (tp) REVERT: A 733 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7595 (mp) REVERT: A 769 LEU cc_start: 0.8406 (mt) cc_final: 0.8190 (tp) REVERT: B 326 ILE cc_start: 0.8796 (pt) cc_final: 0.8556 (mt) REVERT: B 410 GLU cc_start: 0.7680 (tp30) cc_final: 0.7319 (tp30) REVERT: B 444 ASP cc_start: 0.8104 (m-30) cc_final: 0.7763 (t0) REVERT: B 506 LYS cc_start: 0.8309 (pttm) cc_final: 0.7748 (tmtt) REVERT: B 674 ILE cc_start: 0.9331 (mm) cc_final: 0.9122 (mm) REVERT: B 721 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6476 (pt0) REVERT: B 788 GLU cc_start: 0.7035 (tp30) cc_final: 0.6739 (tt0) REVERT: B 806 ASP cc_start: 0.5691 (t70) cc_final: 0.5446 (t70) REVERT: C 52 MET cc_start: 0.8492 (mtp) cc_final: 0.8144 (mtm) REVERT: C 243 LEU cc_start: 0.9006 (tp) cc_final: 0.8741 (tp) REVERT: C 348 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7741 (mt) REVERT: C 405 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7508 (mm) REVERT: C 422 LYS cc_start: 0.7145 (mtpt) cc_final: 0.6714 (mmmm) REVERT: C 429 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6099 (pm20) REVERT: C 482 LYS cc_start: 0.7895 (ptpp) cc_final: 0.7401 (mmmt) REVERT: C 550 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7410 (mmt90) REVERT: C 590 MET cc_start: 0.5333 (mmp) cc_final: 0.5010 (mmp) REVERT: C 597 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7883 (mp0) REVERT: C 688 ARG cc_start: 0.7290 (mtm110) cc_final: 0.7036 (mtp-110) REVERT: D 135 ILE cc_start: 0.8729 (tt) cc_final: 0.8374 (mt) REVERT: D 218 ARG cc_start: 0.7339 (ttt180) cc_final: 0.7058 (tmt170) REVERT: D 235 LYS cc_start: 0.7736 (mttt) cc_final: 0.7519 (ptpt) REVERT: D 422 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7231 (mmtt) REVERT: D 426 ASP cc_start: 0.8056 (t0) cc_final: 0.7800 (t0) REVERT: D 446 VAL cc_start: 0.7671 (m) cc_final: 0.6853 (p) REVERT: D 454 GLU cc_start: 0.7213 (tt0) cc_final: 0.6875 (tp30) REVERT: D 467 GLN cc_start: 0.6990 (mt0) cc_final: 0.6653 (tm-30) REVERT: D 555 LEU cc_start: 0.7017 (mt) cc_final: 0.6808 (mp) REVERT: D 587 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7905 (pp) REVERT: D 590 MET cc_start: 0.6706 (mpp) cc_final: 0.6280 (mpp) REVERT: D 635 PHE cc_start: 0.8426 (m-80) cc_final: 0.8148 (m-80) REVERT: D 686 LYS cc_start: 0.7462 (mttp) cc_final: 0.6933 (mmmm) REVERT: D 753 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5628 (tp) REVERT: E 46 GLN cc_start: 0.8458 (tp40) cc_final: 0.8096 (tm-30) REVERT: E 99 LEU cc_start: 0.8868 (tp) cc_final: 0.8625 (tp) REVERT: E 112 ASN cc_start: 0.8960 (m-40) cc_final: 0.8616 (m-40) REVERT: E 304 LYS cc_start: 0.8324 (tttt) cc_final: 0.8066 (tmtt) REVERT: E 348 GLU cc_start: 0.6544 (mt-10) cc_final: 0.5632 (pm20) REVERT: E 373 MET cc_start: 0.6685 (mtp) cc_final: 0.6402 (ttm) REVERT: E 379 GLN cc_start: 0.7091 (mm110) cc_final: 0.6828 (mm-40) REVERT: F 37 MET cc_start: 0.7930 (ttp) cc_final: 0.7676 (tpp) REVERT: F 44 THR cc_start: 0.8590 (m) cc_final: 0.8188 (p) REVERT: F 330 TYR cc_start: 0.6160 (t80) cc_final: 0.5862 (t80) REVERT: F 343 TYR cc_start: 0.4100 (OUTLIER) cc_final: 0.2418 (m-10) REVERT: G 43 LYS cc_start: 0.6170 (mttp) cc_final: 0.5963 (pttt) REVERT: G 46 GLU cc_start: 0.8817 (tt0) cc_final: 0.8323 (tp30) REVERT: G 56 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7836 (mp0) REVERT: G 104 TYR cc_start: 0.8009 (m-80) cc_final: 0.7433 (m-80) REVERT: H 13 GLN cc_start: 0.6832 (mp10) cc_final: 0.6619 (pp30) REVERT: I 3 GLN cc_start: 0.5550 (pp30) cc_final: 0.4685 (pp30) REVERT: I 45 ARG cc_start: 0.5578 (ttm110) cc_final: 0.5334 (ttp-110) REVERT: I 46 GLU cc_start: 0.8172 (tt0) cc_final: 0.7657 (pm20) REVERT: I 74 ASN cc_start: 0.5986 (m-40) cc_final: 0.5141 (p0) REVERT: I 76 LYS cc_start: 0.7849 (mttm) cc_final: 0.7568 (mptt) REVERT: J 36 TRP cc_start: 0.5893 (m100) cc_final: 0.4899 (m100) REVERT: J 105 TRP cc_start: 0.2548 (m-90) cc_final: 0.2214 (m-10) outliers start: 151 outliers final: 81 residues processed: 555 average time/residue: 0.4377 time to fit residues: 391.7957 Evaluate side-chains 438 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 345 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 343 TYR Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 342 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 304 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN D 431 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN G 110 GLN H 110 GLN I 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 31992 Z= 0.342 Angle : 0.603 8.303 43348 Z= 0.316 Chirality : 0.043 0.166 4903 Planarity : 0.004 0.045 5371 Dihedral : 6.455 73.967 4285 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.65 % Allowed : 13.34 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3759 helix: 0.22 (0.13), residues: 1677 sheet: -0.54 (0.22), residues: 600 loop : -0.58 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 36 HIS 0.017 0.001 HIS J 32 PHE 0.022 0.002 PHE C 390 TYR 0.023 0.002 TYR C 689 ARG 0.005 0.001 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 352 time to evaluate : 3.512 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: A 104 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.8449 (t70) REVERT: A 154 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: A 161 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8287 (pp) REVERT: A 238 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 415 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7789 (ttpm) REVERT: A 426 ASP cc_start: 0.7318 (t0) cc_final: 0.7048 (t0) REVERT: A 516 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7084 (tptp) REVERT: A 546 LEU cc_start: 0.8418 (tp) cc_final: 0.8186 (tp) REVERT: A 593 LEU cc_start: 0.8640 (tt) cc_final: 0.8355 (tt) REVERT: A 597 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7580 (mp0) REVERT: A 626 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 733 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 769 LEU cc_start: 0.8339 (mt) cc_final: 0.8119 (tp) REVERT: B 244 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: B 326 ILE cc_start: 0.8890 (pt) cc_final: 0.8585 (mt) REVERT: B 375 MET cc_start: 0.7755 (mtt) cc_final: 0.7489 (mtt) REVERT: B 410 GLU cc_start: 0.7773 (tp30) cc_final: 0.7405 (tp30) REVERT: B 444 ASP cc_start: 0.8075 (m-30) cc_final: 0.7819 (t0) REVERT: B 506 LYS cc_start: 0.8399 (pttm) cc_final: 0.7793 (tmtt) REVERT: B 674 ILE cc_start: 0.9334 (mm) cc_final: 0.9132 (mm) REVERT: B 689 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 721 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6529 (pt0) REVERT: C 52 MET cc_start: 0.8575 (mtp) cc_final: 0.8285 (mtm) REVERT: C 243 LEU cc_start: 0.8951 (tp) cc_final: 0.8717 (tp) REVERT: C 245 GLU cc_start: 0.8015 (pt0) cc_final: 0.7810 (tp30) REVERT: C 292 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8535 (p0) REVERT: C 377 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7523 (m-70) REVERT: C 405 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7501 (mm) REVERT: C 422 LYS cc_start: 0.7189 (mtpt) cc_final: 0.6904 (mmmm) REVERT: C 429 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6225 (pm20) REVERT: C 482 LYS cc_start: 0.7639 (ptpp) cc_final: 0.7317 (mmmt) REVERT: C 584 LEU cc_start: 0.6939 (mt) cc_final: 0.6438 (tp) REVERT: C 590 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4929 (mmp) REVERT: C 597 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7817 (mp0) REVERT: C 635 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6981 (m-10) REVERT: D 135 ILE cc_start: 0.8855 (tt) cc_final: 0.8513 (mt) REVERT: D 218 ARG cc_start: 0.7353 (ttt180) cc_final: 0.7054 (tmt170) REVERT: D 235 LYS cc_start: 0.7768 (mttt) cc_final: 0.7553 (ptpt) REVERT: D 422 LYS cc_start: 0.7393 (mtpt) cc_final: 0.7188 (mmtt) REVERT: D 446 VAL cc_start: 0.7651 (m) cc_final: 0.6876 (p) REVERT: D 454 GLU cc_start: 0.7188 (tt0) cc_final: 0.6784 (tp30) REVERT: D 467 GLN cc_start: 0.7132 (mt0) cc_final: 0.6676 (tm-30) REVERT: D 587 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7830 (pp) REVERT: D 590 MET cc_start: 0.6937 (mpp) cc_final: 0.6476 (mpp) REVERT: D 635 PHE cc_start: 0.8524 (m-80) cc_final: 0.8259 (m-80) REVERT: D 647 TRP cc_start: 0.6978 (OUTLIER) cc_final: 0.6758 (p90) REVERT: D 686 LYS cc_start: 0.7508 (mttp) cc_final: 0.6888 (mmmm) REVERT: E 20 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6826 (tt) REVERT: E 46 GLN cc_start: 0.8561 (tp40) cc_final: 0.7801 (tm-30) REVERT: E 48 MET cc_start: 0.7890 (ttt) cc_final: 0.7627 (ttm) REVERT: E 348 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5395 (pm20) REVERT: E 379 GLN cc_start: 0.7381 (mm110) cc_final: 0.7108 (mm-40) REVERT: F 37 MET cc_start: 0.8010 (ttp) cc_final: 0.7742 (tpp) REVERT: F 44 THR cc_start: 0.8548 (m) cc_final: 0.8137 (p) REVERT: F 156 GLU cc_start: 0.5218 (OUTLIER) cc_final: 0.4495 (tm-30) REVERT: F 300 MET cc_start: 0.8410 (tpp) cc_final: 0.8045 (mmp) REVERT: F 330 TYR cc_start: 0.6126 (t80) cc_final: 0.5776 (t80) REVERT: G 20 LEU cc_start: 0.5785 (mt) cc_final: 0.5527 (mt) REVERT: G 46 GLU cc_start: 0.8872 (tt0) cc_final: 0.8436 (tp30) REVERT: G 56 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7848 (mp0) REVERT: G 104 TYR cc_start: 0.8156 (m-80) cc_final: 0.7554 (m-80) REVERT: I 3 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.4723 (pp30) REVERT: I 73 ASP cc_start: 0.3774 (OUTLIER) cc_final: 0.3372 (p0) REVERT: I 74 ASN cc_start: 0.6344 (m-40) cc_final: 0.5522 (p0) REVERT: I 76 LYS cc_start: 0.7860 (mttm) cc_final: 0.7503 (mptt) REVERT: J 32 HIS cc_start: 0.6436 (m90) cc_final: 0.6041 (m90) REVERT: J 36 TRP cc_start: 0.5928 (m100) cc_final: 0.4898 (m100) REVERT: J 105 TRP cc_start: 0.2671 (m-90) cc_final: 0.2321 (m-10) outliers start: 196 outliers final: 131 residues processed: 508 average time/residue: 0.4968 time to fit residues: 415.8252 Evaluate side-chains 469 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 316 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain G residue 45 ARG Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 8.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 chunk 325 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 HIS ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** D 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 31992 Z= 0.532 Angle : 0.727 10.830 43348 Z= 0.379 Chirality : 0.047 0.197 4903 Planarity : 0.005 0.063 5371 Dihedral : 6.864 71.284 4275 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 6.85 % Allowed : 14.83 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3759 helix: -0.22 (0.13), residues: 1660 sheet: -0.81 (0.21), residues: 651 loop : -0.75 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 105 HIS 0.011 0.002 HIS F 134 PHE 0.030 0.003 PHE C 353 TYR 0.028 0.002 TYR D 325 ARG 0.008 0.001 ARG C 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 314 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8603 (t70) REVERT: A 154 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: A 238 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 426 ASP cc_start: 0.7315 (t0) cc_final: 0.7072 (t0) REVERT: A 597 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7672 (mp0) REVERT: A 626 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 733 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7595 (mp) REVERT: B 244 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: B 350 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5490 (ttpp) REVERT: B 375 MET cc_start: 0.7883 (mtt) cc_final: 0.7674 (mtt) REVERT: B 380 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 444 ASP cc_start: 0.8058 (m-30) cc_final: 0.7616 (t0) REVERT: B 448 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 506 LYS cc_start: 0.8451 (pttm) cc_final: 0.7886 (tmtt) REVERT: B 689 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 721 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6730 (pt0) REVERT: C 243 LEU cc_start: 0.9012 (tp) cc_final: 0.8755 (tp) REVERT: C 292 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8753 (p0) REVERT: C 377 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (m170) REVERT: C 405 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7609 (mm) REVERT: C 422 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6692 (mmmm) REVERT: C 429 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5958 (pm20) REVERT: C 571 LYS cc_start: 0.6376 (tptp) cc_final: 0.6171 (tptt) REVERT: C 590 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5509 (mmp) REVERT: C 623 ASP cc_start: 0.8374 (t0) cc_final: 0.8120 (t0) REVERT: C 635 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6995 (m-10) REVERT: C 688 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7359 (mtp180) REVERT: D 20 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8092 (mt) REVERT: D 135 ILE cc_start: 0.8844 (tt) cc_final: 0.8519 (mt) REVERT: D 218 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7049 (tmt170) REVERT: D 281 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8422 (p90) REVERT: D 292 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8610 (p0) REVERT: D 297 VAL cc_start: 0.8971 (m) cc_final: 0.8726 (p) REVERT: D 353 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7358 (t80) REVERT: D 422 LYS cc_start: 0.7637 (mtpt) cc_final: 0.7389 (mmtt) REVERT: D 446 VAL cc_start: 0.7652 (m) cc_final: 0.6965 (p) REVERT: D 454 GLU cc_start: 0.7455 (tt0) cc_final: 0.7190 (tt0) REVERT: D 467 GLN cc_start: 0.7069 (mt0) cc_final: 0.6621 (tm-30) REVERT: D 590 MET cc_start: 0.7419 (mpp) cc_final: 0.7099 (mpp) REVERT: D 635 PHE cc_start: 0.8527 (m-80) cc_final: 0.8172 (m-80) REVERT: D 647 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.6661 (p90) REVERT: D 686 LYS cc_start: 0.7491 (mttp) cc_final: 0.6861 (mmmm) REVERT: E 49 GLN cc_start: 0.7189 (mm-40) cc_final: 0.6934 (mm-40) REVERT: E 305 ASN cc_start: 0.7501 (p0) cc_final: 0.6967 (p0) REVERT: E 348 GLU cc_start: 0.6439 (mt-10) cc_final: 0.5406 (pm20) REVERT: E 372 PHE cc_start: 0.7261 (t80) cc_final: 0.6197 (t80) REVERT: E 375 HIS cc_start: 0.4599 (OUTLIER) cc_final: 0.4181 (m-70) REVERT: E 376 MET cc_start: 0.6261 (ptm) cc_final: 0.5659 (mtp) REVERT: E 379 GLN cc_start: 0.7258 (mm110) cc_final: 0.7057 (mm-40) REVERT: F 37 MET cc_start: 0.8048 (ttp) cc_final: 0.7782 (tpp) REVERT: F 44 THR cc_start: 0.8590 (m) cc_final: 0.8167 (p) REVERT: F 103 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8024 (mp) REVERT: F 114 MET cc_start: 0.8933 (tpp) cc_final: 0.8182 (tpp) REVERT: F 156 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.4559 (tm-30) REVERT: G 46 GLU cc_start: 0.8716 (tt0) cc_final: 0.8263 (tp30) REVERT: G 56 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7913 (mp0) REVERT: G 59 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8370 (mm-30) REVERT: G 104 TYR cc_start: 0.8205 (m-80) cc_final: 0.7698 (m-80) REVERT: H 34 MET cc_start: 0.7433 (mmm) cc_final: 0.6765 (ttt) REVERT: I 73 ASP cc_start: 0.3588 (OUTLIER) cc_final: 0.3104 (p0) REVERT: I 74 ASN cc_start: 0.6483 (m-40) cc_final: 0.5689 (p0) REVERT: I 76 LYS cc_start: 0.7916 (mttm) cc_final: 0.7504 (mptt) REVERT: J 31 ARG cc_start: 0.8144 (mtm110) cc_final: 0.7676 (tpt90) REVERT: J 34 MET cc_start: 0.2595 (tpp) cc_final: 0.2228 (tpt) REVERT: J 36 TRP cc_start: 0.5922 (m100) cc_final: 0.4864 (m100) REVERT: J 45 ARG cc_start: 0.4964 (ttm110) cc_final: 0.3904 (ttt180) outliers start: 238 outliers final: 164 residues processed: 513 average time/residue: 0.4136 time to fit residues: 349.5592 Evaluate side-chains 473 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 284 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 380 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 629 ILE Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 280 CYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 411 TRP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 375 HIS Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain F residue 334 CYS Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ASN Chi-restraints excluded: chain J residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 310 optimal weight: 0.0010 chunk 251 optimal weight: 0.0870 chunk 0 optimal weight: 0.5980 chunk 185 optimal weight: 8.9990 chunk 326 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.4364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 31992 Z= 0.152 Angle : 0.521 10.920 43348 Z= 0.273 Chirality : 0.040 0.213 4903 Planarity : 0.003 0.039 5371 Dihedral : 6.290 67.687 4270 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.49 % Allowed : 17.40 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3759 helix: 0.32 (0.13), residues: 1655 sheet: -0.67 (0.21), residues: 648 loop : -0.57 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 24 HIS 0.027 0.001 HIS E 375 PHE 0.024 0.001 PHE A 393 TYR 0.019 0.001 TYR C 477 ARG 0.007 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 344 time to evaluate : 3.913 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 104 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8213 (t70) REVERT: A 154 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 161 LEU cc_start: 0.8548 (tp) cc_final: 0.8275 (pp) REVERT: A 238 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 426 ASP cc_start: 0.7121 (t0) cc_final: 0.6834 (t0) REVERT: A 546 LEU cc_start: 0.8342 (tp) cc_final: 0.8109 (tp) REVERT: A 597 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7607 (mp0) REVERT: B 244 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.5705 (m-80) REVERT: B 326 ILE cc_start: 0.8870 (pt) cc_final: 0.8383 (mt) REVERT: B 350 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5447 (ttpp) REVERT: B 410 GLU cc_start: 0.7699 (tp30) cc_final: 0.7425 (tp30) REVERT: B 444 ASP cc_start: 0.8018 (m-30) cc_final: 0.7691 (t0) REVERT: B 506 LYS cc_start: 0.8346 (pttm) cc_final: 0.7776 (tmtt) REVERT: B 689 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 721 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6742 (pt0) REVERT: B 791 PHE cc_start: 0.6645 (t80) cc_final: 0.5957 (t80) REVERT: C 243 LEU cc_start: 0.8958 (tp) cc_final: 0.8724 (tp) REVERT: C 245 GLU cc_start: 0.8064 (pt0) cc_final: 0.7762 (tp30) REVERT: C 292 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8363 (p0) REVERT: C 377 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7389 (m170) REVERT: C 405 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7543 (mm) REVERT: C 422 LYS cc_start: 0.6993 (mtpt) cc_final: 0.6674 (mmmm) REVERT: C 429 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6231 (pm20) REVERT: C 482 LYS cc_start: 0.7487 (ptpp) cc_final: 0.7199 (tttt) REVERT: C 590 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5579 (mmp) REVERT: C 597 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: D 135 ILE cc_start: 0.8766 (tt) cc_final: 0.8392 (mt) REVERT: D 218 ARG cc_start: 0.7285 (ttt180) cc_final: 0.6995 (tmt170) REVERT: D 297 VAL cc_start: 0.8878 (m) cc_final: 0.8665 (p) REVERT: D 325 TYR cc_start: 0.8618 (t80) cc_final: 0.8405 (t80) REVERT: D 446 VAL cc_start: 0.7671 (m) cc_final: 0.6977 (p) REVERT: D 467 GLN cc_start: 0.7130 (mt0) cc_final: 0.6720 (tm-30) REVERT: D 590 MET cc_start: 0.7628 (mpp) cc_final: 0.7401 (mpp) REVERT: D 635 PHE cc_start: 0.8614 (m-80) cc_final: 0.8396 (m-80) REVERT: D 647 TRP cc_start: 0.7077 (OUTLIER) cc_final: 0.6821 (p90) REVERT: D 686 LYS cc_start: 0.7419 (mttp) cc_final: 0.6802 (mmmm) REVERT: E 49 GLN cc_start: 0.7241 (mm-40) cc_final: 0.7031 (mm-40) REVERT: E 112 ASN cc_start: 0.8954 (m-40) cc_final: 0.8698 (m110) REVERT: E 113 GLN cc_start: 0.7640 (mt0) cc_final: 0.6831 (mt0) REVERT: E 248 PHE cc_start: 0.6738 (t80) cc_final: 0.6328 (t80) REVERT: E 305 ASN cc_start: 0.7636 (p0) cc_final: 0.7088 (p0) REVERT: E 312 MET cc_start: 0.7467 (ptp) cc_final: 0.7182 (ptt) REVERT: E 348 GLU cc_start: 0.6436 (mt-10) cc_final: 0.5402 (pm20) REVERT: E 372 PHE cc_start: 0.7181 (t80) cc_final: 0.6947 (t80) REVERT: E 379 GLN cc_start: 0.7319 (mm110) cc_final: 0.7116 (mm-40) REVERT: F 37 MET cc_start: 0.7997 (ttp) cc_final: 0.7745 (tpp) REVERT: F 44 THR cc_start: 0.8545 (m) cc_final: 0.8143 (p) REVERT: F 114 MET cc_start: 0.8713 (tpp) cc_final: 0.8460 (mmm) REVERT: F 156 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4885 (tm-30) REVERT: F 300 MET cc_start: 0.8418 (tpp) cc_final: 0.7982 (mmp) REVERT: F 330 TYR cc_start: 0.5769 (t80) cc_final: 0.5542 (t80) REVERT: G 46 GLU cc_start: 0.8837 (tt0) cc_final: 0.8346 (tp30) REVERT: G 56 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7753 (mp0) REVERT: G 59 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7973 (mm-30) REVERT: G 104 TYR cc_start: 0.8157 (m-80) cc_final: 0.7589 (m-80) REVERT: I 73 ASP cc_start: 0.3787 (OUTLIER) cc_final: 0.3587 (p0) REVERT: I 74 ASN cc_start: 0.6109 (m-40) cc_final: 0.5169 (p0) REVERT: I 76 LYS cc_start: 0.7756 (mttm) cc_final: 0.7378 (mptt) REVERT: J 31 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7390 (tpt90) REVERT: J 36 TRP cc_start: 0.5887 (m100) cc_final: 0.4869 (m100) REVERT: J 105 TRP cc_start: 0.2554 (m-90) cc_final: 0.2206 (m-10) outliers start: 156 outliers final: 106 residues processed: 471 average time/residue: 0.4424 time to fit residues: 348.6369 Evaluate side-chains 427 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 306 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 597 GLU Chi-restraints excluded: chain C residue 639 HIS Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 2.9990 chunk 327 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 363 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31992 Z= 0.178 Angle : 0.513 9.372 43348 Z= 0.269 Chirality : 0.040 0.192 4903 Planarity : 0.003 0.040 5371 Dihedral : 6.157 70.159 4270 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.84 % Allowed : 17.31 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3759 helix: 0.49 (0.13), residues: 1632 sheet: -0.71 (0.21), residues: 627 loop : -0.41 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 340 HIS 0.007 0.001 HIS F 134 PHE 0.024 0.001 PHE F 41 TYR 0.020 0.001 TYR C 477 ARG 0.006 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 329 time to evaluate : 3.758 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: A 104 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8319 (t70) REVERT: A 154 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: A 238 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 426 ASP cc_start: 0.7227 (t0) cc_final: 0.6977 (t0) REVERT: A 546 LEU cc_start: 0.8327 (tp) cc_final: 0.8089 (tp) REVERT: A 597 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7530 (mp0) REVERT: B 244 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5790 (m-80) REVERT: B 326 ILE cc_start: 0.8872 (pt) cc_final: 0.8403 (mt) REVERT: B 350 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5429 (ttpp) REVERT: B 410 GLU cc_start: 0.7670 (tp30) cc_final: 0.7366 (tp30) REVERT: B 444 ASP cc_start: 0.8057 (m-30) cc_final: 0.7718 (t0) REVERT: B 448 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 506 LYS cc_start: 0.8347 (pttm) cc_final: 0.7782 (tmtt) REVERT: B 590 MET cc_start: 0.8431 (mmm) cc_final: 0.8005 (mmm) REVERT: B 689 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 791 PHE cc_start: 0.6638 (t80) cc_final: 0.5898 (t80) REVERT: C 243 LEU cc_start: 0.8985 (tp) cc_final: 0.8734 (tp) REVERT: C 281 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8715 (p90) REVERT: C 353 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6746 (t80) REVERT: C 377 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.6966 (m170) REVERT: C 405 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7523 (mm) REVERT: C 422 LYS cc_start: 0.7006 (mtpt) cc_final: 0.6670 (mmmm) REVERT: C 429 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: C 482 LYS cc_start: 0.7578 (ptpp) cc_final: 0.7239 (tttt) REVERT: C 590 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5595 (mmp) REVERT: C 635 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: D 135 ILE cc_start: 0.8800 (tt) cc_final: 0.8419 (mt) REVERT: D 218 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6984 (tmt170) REVERT: D 297 VAL cc_start: 0.8859 (m) cc_final: 0.8640 (p) REVERT: D 325 TYR cc_start: 0.8643 (t80) cc_final: 0.8438 (t80) REVERT: D 446 VAL cc_start: 0.7682 (m) cc_final: 0.6956 (p) REVERT: D 467 GLN cc_start: 0.6995 (mt0) cc_final: 0.6692 (tm-30) REVERT: D 590 MET cc_start: 0.7613 (mpp) cc_final: 0.7358 (mpp) REVERT: D 635 PHE cc_start: 0.8625 (m-80) cc_final: 0.8411 (m-80) REVERT: D 647 TRP cc_start: 0.7060 (OUTLIER) cc_final: 0.6819 (p90) REVERT: D 686 LYS cc_start: 0.7522 (mttp) cc_final: 0.6891 (mmmm) REVERT: E 49 GLN cc_start: 0.7238 (mm-40) cc_final: 0.7027 (mm-40) REVERT: E 112 ASN cc_start: 0.8967 (m-40) cc_final: 0.8756 (m110) REVERT: E 157 HIS cc_start: 0.5618 (m170) cc_final: 0.5287 (m170) REVERT: E 248 PHE cc_start: 0.6776 (t80) cc_final: 0.6347 (t80) REVERT: E 305 ASN cc_start: 0.7602 (p0) cc_final: 0.7203 (p0) REVERT: E 348 GLU cc_start: 0.6349 (mt-10) cc_final: 0.5308 (pm20) REVERT: E 372 PHE cc_start: 0.7180 (t80) cc_final: 0.6910 (t80) REVERT: F 37 MET cc_start: 0.7999 (ttp) cc_final: 0.7740 (tpp) REVERT: F 44 THR cc_start: 0.8486 (m) cc_final: 0.8074 (p) REVERT: F 156 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.4908 (tm-30) REVERT: F 300 MET cc_start: 0.8402 (tpp) cc_final: 0.8014 (mmp) REVERT: F 330 TYR cc_start: 0.5854 (t80) cc_final: 0.5619 (t80) REVERT: G 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8341 (tp30) REVERT: G 56 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7698 (mp0) REVERT: G 59 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8176 (mm-30) REVERT: H 34 MET cc_start: 0.7284 (mmt) cc_final: 0.6603 (mmp) REVERT: I 32 HIS cc_start: 0.5910 (OUTLIER) cc_final: 0.4636 (m-70) REVERT: I 36 TRP cc_start: 0.5862 (m100) cc_final: 0.5428 (m100) REVERT: I 73 ASP cc_start: 0.3804 (OUTLIER) cc_final: 0.3586 (p0) REVERT: I 74 ASN cc_start: 0.6103 (m-40) cc_final: 0.5160 (p0) REVERT: I 76 LYS cc_start: 0.7747 (mttm) cc_final: 0.7371 (mptt) REVERT: J 36 TRP cc_start: 0.5609 (m100) cc_final: 0.4746 (m100) REVERT: J 51 ILE cc_start: 0.2396 (tp) cc_final: 0.1511 (mm) REVERT: J 105 TRP cc_start: 0.2640 (m-90) cc_final: 0.2414 (m-10) outliers start: 168 outliers final: 118 residues processed: 467 average time/residue: 0.4051 time to fit residues: 315.4290 Evaluate side-chains 444 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 309 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 362 optimal weight: 0.7980 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31992 Z= 0.235 Angle : 0.540 9.806 43348 Z= 0.282 Chirality : 0.041 0.182 4903 Planarity : 0.003 0.055 5371 Dihedral : 6.113 71.122 4266 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.93 % Allowed : 17.43 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3759 helix: 0.47 (0.13), residues: 1626 sheet: -0.75 (0.21), residues: 627 loop : -0.44 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 24 HIS 0.007 0.001 HIS F 134 PHE 0.025 0.001 PHE F 41 TYR 0.016 0.001 TYR E 279 ARG 0.005 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 319 time to evaluate : 3.975 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: A 104 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8313 (t70) REVERT: A 154 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: A 238 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 426 ASP cc_start: 0.7375 (t0) cc_final: 0.7106 (t0) REVERT: A 546 LEU cc_start: 0.8344 (tp) cc_final: 0.8132 (tp) REVERT: A 597 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7563 (mp0) REVERT: B 244 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.5698 (m-80) REVERT: B 265 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6947 (tpt) REVERT: B 326 ILE cc_start: 0.8895 (pt) cc_final: 0.8406 (mt) REVERT: B 350 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5465 (ttpp) REVERT: B 410 GLU cc_start: 0.7744 (tp30) cc_final: 0.7443 (tp30) REVERT: B 444 ASP cc_start: 0.8048 (m-30) cc_final: 0.7738 (t0) REVERT: B 448 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8734 (tt) REVERT: B 506 LYS cc_start: 0.8347 (pttm) cc_final: 0.7787 (tmtt) REVERT: B 590 MET cc_start: 0.8442 (mmm) cc_final: 0.8005 (mmm) REVERT: B 689 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: B 791 PHE cc_start: 0.6697 (t80) cc_final: 0.5969 (t80) REVERT: C 292 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8380 (p0) REVERT: C 353 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6773 (t80) REVERT: C 377 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7036 (m170) REVERT: C 405 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7517 (mm) REVERT: C 422 LYS cc_start: 0.7005 (mtpt) cc_final: 0.6675 (mmmm) REVERT: C 429 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: C 482 LYS cc_start: 0.7536 (ptpp) cc_final: 0.7262 (tttt) REVERT: C 590 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5790 (mmp) REVERT: C 635 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7076 (m-10) REVERT: C 644 LEU cc_start: 0.6525 (tp) cc_final: 0.6324 (tp) REVERT: C 688 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7783 (ptm160) REVERT: C 764 ASN cc_start: 0.6045 (OUTLIER) cc_final: 0.4657 (t0) REVERT: D 135 ILE cc_start: 0.8831 (tt) cc_final: 0.8465 (mt) REVERT: D 218 ARG cc_start: 0.7302 (ttt180) cc_final: 0.6978 (tmt170) REVERT: D 297 VAL cc_start: 0.8863 (m) cc_final: 0.8655 (p) REVERT: D 446 VAL cc_start: 0.7673 (m) cc_final: 0.6946 (p) REVERT: D 467 GLN cc_start: 0.7037 (mt0) cc_final: 0.6658 (tm-30) REVERT: D 590 MET cc_start: 0.7661 (mpp) cc_final: 0.7352 (mpp) REVERT: D 635 PHE cc_start: 0.8610 (m-80) cc_final: 0.8180 (m-80) REVERT: D 647 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6829 (p90) REVERT: D 686 LYS cc_start: 0.7597 (mttp) cc_final: 0.6932 (mmmm) REVERT: E 117 GLU cc_start: 0.8072 (tp30) cc_final: 0.7763 (tp30) REVERT: E 305 ASN cc_start: 0.7610 (p0) cc_final: 0.7178 (p0) REVERT: E 348 GLU cc_start: 0.5170 (mt-10) cc_final: 0.4956 (pm20) REVERT: E 372 PHE cc_start: 0.7214 (t80) cc_final: 0.6910 (t80) REVERT: F 37 MET cc_start: 0.7924 (ttp) cc_final: 0.7677 (tpp) REVERT: F 44 THR cc_start: 0.8486 (m) cc_final: 0.8069 (p) REVERT: F 156 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.4940 (tm-30) REVERT: F 300 MET cc_start: 0.8409 (tpp) cc_final: 0.7953 (mmp) REVERT: G 46 GLU cc_start: 0.8860 (tt0) cc_final: 0.8339 (tp30) REVERT: G 56 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7876 (mp0) REVERT: G 59 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8352 (mm-30) REVERT: H 27 PHE cc_start: 0.6086 (p90) cc_final: 0.5685 (p90) REVERT: H 34 MET cc_start: 0.7380 (mmt) cc_final: 0.6694 (mmp) REVERT: I 32 HIS cc_start: 0.5964 (OUTLIER) cc_final: 0.4867 (m-70) REVERT: I 37 TYR cc_start: 0.6132 (m-10) cc_final: 0.5929 (m-10) REVERT: I 74 ASN cc_start: 0.6118 (m-40) cc_final: 0.5177 (p0) REVERT: I 76 LYS cc_start: 0.7751 (mttm) cc_final: 0.7372 (mptt) REVERT: J 36 TRP cc_start: 0.5720 (m100) cc_final: 0.4825 (m100) outliers start: 171 outliers final: 132 residues processed: 459 average time/residue: 0.4062 time to fit residues: 311.3790 Evaluate side-chains 450 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 300 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 393 PHE Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.0070 chunk 230 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 560 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 31992 Z= 0.152 Angle : 0.511 11.824 43348 Z= 0.266 Chirality : 0.040 0.214 4903 Planarity : 0.003 0.061 5371 Dihedral : 5.842 68.800 4262 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.12 % Allowed : 18.38 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3759 helix: 0.46 (0.13), residues: 1680 sheet: -0.59 (0.20), residues: 668 loop : -0.53 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 36 HIS 0.008 0.001 HIS F 134 PHE 0.024 0.001 PHE E 248 TYR 0.026 0.001 TYR D 325 ARG 0.010 0.000 ARG J 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 333 time to evaluate : 3.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.9032 (OUTLIER) cc_final: 0.8160 (t70) REVERT: A 154 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 161 LEU cc_start: 0.8520 (tp) cc_final: 0.8278 (pp) REVERT: A 238 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8137 (mm-30) REVERT: A 265 MET cc_start: 0.7982 (ttt) cc_final: 0.7765 (ttp) REVERT: A 426 ASP cc_start: 0.7230 (t0) cc_final: 0.6993 (t0) REVERT: A 597 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7562 (mp0) REVERT: B 244 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: B 265 MET cc_start: 0.7343 (tpt) cc_final: 0.7059 (tpt) REVERT: B 326 ILE cc_start: 0.8869 (pt) cc_final: 0.8397 (mt) REVERT: B 337 MET cc_start: 0.7013 (ppp) cc_final: 0.6705 (mmt) REVERT: B 410 GLU cc_start: 0.7683 (tp30) cc_final: 0.7362 (tp30) REVERT: B 444 ASP cc_start: 0.8066 (m-30) cc_final: 0.7750 (t0) REVERT: B 506 LYS cc_start: 0.8358 (pttm) cc_final: 0.7785 (tmtt) REVERT: B 590 MET cc_start: 0.8387 (mmm) cc_final: 0.7923 (mmm) REVERT: B 674 ILE cc_start: 0.9322 (mm) cc_final: 0.9076 (mm) REVERT: B 689 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7613 (m-80) REVERT: B 800 GLU cc_start: 0.7732 (pt0) cc_final: 0.7396 (pt0) REVERT: C 160 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7942 (mm) REVERT: C 245 GLU cc_start: 0.8071 (pt0) cc_final: 0.7835 (tp30) REVERT: C 292 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8281 (p0) REVERT: C 353 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 377 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.6913 (m170) REVERT: C 405 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (mm) REVERT: C 422 LYS cc_start: 0.7007 (mtpt) cc_final: 0.6668 (mmmm) REVERT: C 429 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: C 482 LYS cc_start: 0.7519 (ptpp) cc_final: 0.7237 (tttt) REVERT: C 590 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5875 (mmp) REVERT: D 135 ILE cc_start: 0.8780 (tt) cc_final: 0.8396 (mt) REVERT: D 218 ARG cc_start: 0.7294 (ttt180) cc_final: 0.6969 (tmt170) REVERT: D 297 VAL cc_start: 0.8830 (m) cc_final: 0.8623 (p) REVERT: D 446 VAL cc_start: 0.7630 (m) cc_final: 0.6880 (p) REVERT: D 459 VAL cc_start: 0.6876 (OUTLIER) cc_final: 0.6577 (p) REVERT: D 467 GLN cc_start: 0.7115 (mt0) cc_final: 0.6690 (tm-30) REVERT: D 590 MET cc_start: 0.7634 (mpp) cc_final: 0.7332 (mpp) REVERT: D 635 PHE cc_start: 0.8625 (m-80) cc_final: 0.8153 (m-80) REVERT: D 686 LYS cc_start: 0.7527 (mttp) cc_final: 0.6959 (mmmm) REVERT: E 305 ASN cc_start: 0.7511 (p0) cc_final: 0.7103 (p0) REVERT: E 348 GLU cc_start: 0.5278 (mt-10) cc_final: 0.5071 (pm20) REVERT: E 372 PHE cc_start: 0.7179 (t80) cc_final: 0.6866 (t80) REVERT: F 37 MET cc_start: 0.7912 (ttp) cc_final: 0.7671 (tpp) REVERT: F 44 THR cc_start: 0.8441 (m) cc_final: 0.8039 (p) REVERT: F 156 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.4941 (tm-30) REVERT: F 300 MET cc_start: 0.8417 (tpp) cc_final: 0.7963 (mmp) REVERT: G 46 GLU cc_start: 0.8863 (tt0) cc_final: 0.8333 (tp30) REVERT: G 56 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7670 (mp0) REVERT: G 59 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8307 (mm-30) REVERT: H 27 PHE cc_start: 0.5934 (p90) cc_final: 0.5533 (p90) REVERT: H 34 MET cc_start: 0.7347 (mmt) cc_final: 0.6634 (mmp) REVERT: H 68 PHE cc_start: 0.8125 (m-10) cc_final: 0.7371 (m-10) REVERT: I 32 HIS cc_start: 0.5800 (OUTLIER) cc_final: 0.4179 (m-70) REVERT: I 67 ARG cc_start: 0.5073 (mtp180) cc_final: 0.4712 (mtp180) REVERT: I 76 LYS cc_start: 0.7618 (mttm) cc_final: 0.7367 (mptt) REVERT: J 36 TRP cc_start: 0.5654 (m100) cc_final: 0.4851 (m100) outliers start: 143 outliers final: 112 residues processed: 455 average time/residue: 0.3921 time to fit residues: 297.5403 Evaluate side-chains 437 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 311 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 0.6980 chunk 347 optimal weight: 0.9990 chunk 316 optimal weight: 0.8980 chunk 337 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 147 optimal weight: 0.0670 chunk 265 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 319 optimal weight: 0.5980 chunk 336 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 408 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31992 Z= 0.161 Angle : 0.517 11.780 43348 Z= 0.268 Chirality : 0.040 0.208 4903 Planarity : 0.003 0.054 5371 Dihedral : 5.693 69.565 4254 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 19.04 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3759 helix: 0.52 (0.13), residues: 1676 sheet: -0.44 (0.21), residues: 640 loop : -0.57 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 647 HIS 0.005 0.001 HIS F 134 PHE 0.025 0.001 PHE F 41 TYR 0.035 0.001 TYR D 325 ARG 0.008 0.000 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 323 time to evaluate : 4.010 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: A 104 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8200 (t70) REVERT: A 154 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 161 LEU cc_start: 0.8450 (tp) cc_final: 0.8218 (pp) REVERT: A 265 MET cc_start: 0.7970 (ttt) cc_final: 0.7744 (ttp) REVERT: A 426 ASP cc_start: 0.7243 (t0) cc_final: 0.7012 (t0) REVERT: A 597 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7543 (mp0) REVERT: B 115 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7828 (tp30) REVERT: B 244 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.5560 (m-80) REVERT: B 326 ILE cc_start: 0.8783 (pt) cc_final: 0.8451 (mt) REVERT: B 410 GLU cc_start: 0.7661 (tp30) cc_final: 0.7349 (tp30) REVERT: B 444 ASP cc_start: 0.8065 (m-30) cc_final: 0.7756 (t0) REVERT: B 448 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8737 (tt) REVERT: B 506 LYS cc_start: 0.8364 (pttm) cc_final: 0.7786 (tmtt) REVERT: B 590 MET cc_start: 0.8393 (mmm) cc_final: 0.7926 (mmm) REVERT: B 674 ILE cc_start: 0.9319 (mm) cc_final: 0.9072 (mm) REVERT: B 689 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: B 800 GLU cc_start: 0.7820 (pt0) cc_final: 0.7526 (pt0) REVERT: C 160 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 292 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8318 (p0) REVERT: C 353 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6694 (t80) REVERT: C 377 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.6743 (m170) REVERT: C 405 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7459 (mm) REVERT: C 422 LYS cc_start: 0.6921 (mtpt) cc_final: 0.6567 (mmmm) REVERT: C 429 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: C 482 LYS cc_start: 0.7421 (ptpp) cc_final: 0.7175 (tttt) REVERT: C 590 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5858 (mmp) REVERT: D 104 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7716 (t70) REVERT: D 135 ILE cc_start: 0.8800 (tt) cc_final: 0.8416 (mt) REVERT: D 218 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6961 (tmt170) REVERT: D 446 VAL cc_start: 0.7637 (m) cc_final: 0.6867 (p) REVERT: D 459 VAL cc_start: 0.6880 (OUTLIER) cc_final: 0.6580 (p) REVERT: D 467 GLN cc_start: 0.7099 (mt0) cc_final: 0.6653 (tm-30) REVERT: D 587 LEU cc_start: 0.8760 (mm) cc_final: 0.7896 (pp) REVERT: D 590 MET cc_start: 0.7612 (mpp) cc_final: 0.7293 (mpp) REVERT: D 635 PHE cc_start: 0.8644 (m-80) cc_final: 0.8316 (m-80) REVERT: D 686 LYS cc_start: 0.7631 (mttp) cc_final: 0.7034 (mmmm) REVERT: E 305 ASN cc_start: 0.7529 (p0) cc_final: 0.7129 (p0) REVERT: E 372 PHE cc_start: 0.7224 (t80) cc_final: 0.6906 (t80) REVERT: F 37 MET cc_start: 0.7913 (ttp) cc_final: 0.7658 (tpp) REVERT: F 44 THR cc_start: 0.8451 (m) cc_final: 0.8040 (p) REVERT: F 114 MET cc_start: 0.8896 (mmm) cc_final: 0.8393 (tpt) REVERT: F 156 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5502 (tm-30) REVERT: F 300 MET cc_start: 0.8407 (tpp) cc_final: 0.8019 (mmp) REVERT: G 46 GLU cc_start: 0.8910 (tt0) cc_final: 0.8384 (tp30) REVERT: G 56 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7671 (mp0) REVERT: H 34 MET cc_start: 0.7349 (mmt) cc_final: 0.6646 (mmp) REVERT: H 68 PHE cc_start: 0.8219 (m-10) cc_final: 0.7491 (m-10) REVERT: I 32 HIS cc_start: 0.5422 (OUTLIER) cc_final: 0.4246 (m-70) REVERT: I 67 ARG cc_start: 0.5074 (mtp180) cc_final: 0.4716 (mtp180) REVERT: I 76 LYS cc_start: 0.7631 (mttm) cc_final: 0.7377 (mptt) REVERT: J 36 TRP cc_start: 0.5610 (m100) cc_final: 0.4933 (m100) outliers start: 135 outliers final: 111 residues processed: 438 average time/residue: 0.4178 time to fit residues: 305.5954 Evaluate side-chains 431 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 304 time to evaluate : 3.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 0.9980 chunk 357 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 230 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 31992 Z= 0.328 Angle : 0.600 11.893 43348 Z= 0.312 Chirality : 0.043 0.365 4903 Planarity : 0.004 0.053 5371 Dihedral : 5.923 71.946 4250 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.06 % Allowed : 18.95 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3759 helix: 0.35 (0.13), residues: 1657 sheet: -0.57 (0.21), residues: 640 loop : -0.67 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 647 HIS 0.007 0.001 HIS F 134 PHE 0.027 0.002 PHE F 41 TYR 0.053 0.002 TYR D 325 ARG 0.008 0.000 ARG C 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 306 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8330 (t70) REVERT: A 154 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: A 265 MET cc_start: 0.8009 (ttt) cc_final: 0.7805 (ttp) REVERT: A 426 ASP cc_start: 0.7314 (t0) cc_final: 0.7078 (t0) REVERT: A 597 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7535 (mp0) REVERT: B 244 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: B 326 ILE cc_start: 0.8852 (pt) cc_final: 0.8477 (mt) REVERT: B 410 GLU cc_start: 0.7779 (tp30) cc_final: 0.7483 (tp30) REVERT: B 444 ASP cc_start: 0.8069 (m-30) cc_final: 0.7756 (t0) REVERT: B 448 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8716 (tt) REVERT: B 506 LYS cc_start: 0.8350 (pttm) cc_final: 0.7794 (tmtt) REVERT: B 590 MET cc_start: 0.8373 (mmm) cc_final: 0.7925 (mmm) REVERT: B 674 ILE cc_start: 0.9276 (mm) cc_final: 0.9027 (mm) REVERT: B 689 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: C 292 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8454 (p0) REVERT: C 353 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.7021 (t80) REVERT: C 377 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7090 (m170) REVERT: C 405 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7557 (mm) REVERT: C 422 LYS cc_start: 0.7014 (mtpt) cc_final: 0.6672 (mmmm) REVERT: C 429 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6268 (pm20) REVERT: C 482 LYS cc_start: 0.7513 (ptpp) cc_final: 0.7305 (tttt) REVERT: C 590 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5828 (mmp) REVERT: D 135 ILE cc_start: 0.8878 (tt) cc_final: 0.8553 (mt) REVERT: D 218 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6965 (tmt170) REVERT: D 446 VAL cc_start: 0.7632 (m) cc_final: 0.6901 (p) REVERT: D 467 GLN cc_start: 0.7169 (mt0) cc_final: 0.6729 (tm-30) REVERT: D 587 LEU cc_start: 0.8704 (mm) cc_final: 0.7969 (pp) REVERT: D 590 MET cc_start: 0.7554 (mpp) cc_final: 0.7157 (mpp) REVERT: D 686 LYS cc_start: 0.7713 (mttp) cc_final: 0.7014 (mmmm) REVERT: E 117 GLU cc_start: 0.8015 (tp30) cc_final: 0.7734 (tp30) REVERT: E 305 ASN cc_start: 0.7642 (p0) cc_final: 0.7133 (p0) REVERT: E 372 PHE cc_start: 0.7225 (t80) cc_final: 0.6897 (t80) REVERT: F 37 MET cc_start: 0.7904 (ttp) cc_final: 0.7690 (tpp) REVERT: F 44 THR cc_start: 0.8523 (m) cc_final: 0.8109 (p) REVERT: F 156 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.5022 (tm-30) REVERT: F 300 MET cc_start: 0.8454 (tpp) cc_final: 0.8005 (mmp) REVERT: F 309 ASN cc_start: 0.8379 (m-40) cc_final: 0.7972 (t0) REVERT: G 46 GLU cc_start: 0.8857 (tt0) cc_final: 0.8339 (tp30) REVERT: G 56 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7731 (mp0) REVERT: H 34 MET cc_start: 0.7243 (mmt) cc_final: 0.6514 (ttm) REVERT: I 32 HIS cc_start: 0.5529 (OUTLIER) cc_final: 0.4260 (m-70) REVERT: I 67 ARG cc_start: 0.4906 (mtp180) cc_final: 0.4677 (mtp180) REVERT: J 36 TRP cc_start: 0.5873 (m100) cc_final: 0.5112 (m100) REVERT: J 51 ILE cc_start: 0.3755 (tt) cc_final: 0.2957 (mt) outliers start: 141 outliers final: 119 residues processed: 425 average time/residue: 0.4109 time to fit residues: 294.1480 Evaluate side-chains 428 residues out of total 3474 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 296 time to evaluate : 3.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 244 PHE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 730 CYS Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 670 ASN Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 322 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 83 MET Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 275 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 298 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** D 592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.116068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.077497 restraints weight = 80408.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079506 restraints weight = 46016.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079179 restraints weight = 28160.639| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 31992 Z= 0.364 Angle : 0.711 59.197 43348 Z= 0.388 Chirality : 0.042 0.412 4903 Planarity : 0.004 0.054 5371 Dihedral : 5.920 71.998 4250 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.09 % Allowed : 19.01 % Favored : 76.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3759 helix: 0.35 (0.13), residues: 1657 sheet: -0.58 (0.21), residues: 640 loop : -0.68 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 647 HIS 0.007 0.001 HIS F 134 PHE 0.069 0.002 PHE D 635 TYR 0.043 0.002 TYR D 325 ARG 0.013 0.000 ARG C 688 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6927.52 seconds wall clock time: 127 minutes 51.30 seconds (7671.30 seconds total)