Starting phenix.real_space_refine on Fri Jun 27 03:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_15836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_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/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_15836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_15836.map" model { file = "/net/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_15836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b41_15836/06_2025/8b41_15836.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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. Time to flip 16 residue(s): 0.97s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.42, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 4.0 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: 3.91 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: 13.79 Time building geometry restraints manager: 8.91 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: 0.00 - 1.43: 42564 1.43 - 2.86: 668 2.86 - 4.29: 95 4.29 - 5.72: 17 5.72 - 7.15: 4 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 3.040 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR C 679 " pdb=" OD2 ASP C 703 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR D 48 " pdb=" OE1 GLN D 49 " model vdw 2.223 3.040 nonbonded pdb=" NH1 ARG A 419 " pdb=" O HIS A 431 " model vdw 2.228 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.630 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: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.240 Set scattering table: 0.260 Process input model: 70.790 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.160 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.670 ------------------------------------------------------------------------------- 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 32012 Z= 0.121 Angle : 0.482 7.151 43388 Z= 0.273 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 Details of bonding type rmsd hydrogen bonds : bond 0.16010 ( 1482) hydrogen bonds : angle 5.93134 ( 3882) SS BOND : bond 0.00355 ( 20) SS BOND : angle 0.80367 ( 40) covalent geometry : bond 0.00245 (31992) covalent geometry : angle 0.48189 (43348) *********************** 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 to be fit. rotamer outliers: 163 poor density : 610 time to evaluate : 4.161 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: 0.4485 time to fit residues: 528.9038 Evaluate side-chains 444 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 356 time to evaluate : 3.437 ------------------------------------------------------------------------------- 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: 0.5980 chunk 284 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.0970 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 294 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 406 ASN A 467 GLN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN B 105 GLN B 406 ASN B 570 GLN B 592 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN C 105 GLN C 408 ASN C 409 ASN C 431 HIS D 418 GLN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 740 ASN D 741 ASN E 46 GLN E 106 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN E 379 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS H 74 ASN H 110 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.118427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080086 restraints weight = 78793.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081733 restraints weight = 44230.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081210 restraints weight = 27564.475| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 32012 Z= 0.133 Angle : 0.564 10.054 43388 Z= 0.296 Chirality : 0.041 0.186 4903 Planarity : 0.004 0.037 5371 Dihedral : 7.250 70.670 4343 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.61 % Allowed : 12.59 % Favored : 82.81 % 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: -0.28 (0.14), residues: 3759 helix: 0.34 (0.13), residues: 1665 sheet: -0.40 (0.21), residues: 640 loop : -0.53 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 145 HIS 0.010 0.001 HIS J 32 PHE 0.022 0.001 PHE B 250 TYR 0.022 0.001 TYR D 325 ARG 0.007 0.000 ARG J 45 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 1482) hydrogen bonds : angle 4.66435 ( 3882) SS BOND : bond 0.00354 ( 20) SS BOND : angle 0.87722 ( 40) covalent geometry : bond 0.00296 (31992) covalent geometry : angle 0.56362 (43348) *********************** 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 578 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 418 time to evaluate : 3.554 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: A 104 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8416 (t70) REVERT: A 154 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: A 161 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8272 (pp) REVERT: A 238 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 329 VAL cc_start: 0.9054 (t) cc_final: 0.8819 (p) REVERT: A 410 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: A 426 ASP cc_start: 0.7105 (t0) cc_final: 0.6833 (t0) REVERT: A 546 LEU cc_start: 0.8309 (tp) cc_final: 0.8042 (tp) REVERT: A 626 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 687 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 733 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7523 (mp) REVERT: A 769 LEU cc_start: 0.8397 (mt) cc_final: 0.8160 (tp) REVERT: B 226 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6622 (mmm-85) REVERT: B 326 ILE cc_start: 0.8880 (pt) cc_final: 0.8559 (mt) REVERT: B 337 MET cc_start: 0.7424 (ppp) cc_final: 0.7201 (ppp) REVERT: B 410 GLU cc_start: 0.7644 (tp30) cc_final: 0.7285 (tp30) REVERT: B 444 ASP cc_start: 0.7989 (m-30) cc_final: 0.7759 (t0) REVERT: B 506 LYS cc_start: 0.8277 (pttm) cc_final: 0.7730 (tmtt) REVERT: B 674 ILE cc_start: 0.9291 (mm) cc_final: 0.9076 (mm) REVERT: B 689 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7635 (m-80) REVERT: B 721 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6469 (pt0) REVERT: B 806 ASP cc_start: 0.5696 (t70) cc_final: 0.5451 (t70) REVERT: C 52 MET cc_start: 0.8403 (mtp) cc_final: 0.8149 (mtm) REVERT: C 110 ASP cc_start: 0.7886 (m-30) cc_final: 0.7578 (t0) REVERT: C 243 LEU cc_start: 0.9042 (tp) cc_final: 0.8779 (tp) REVERT: C 348 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7952 (mp) REVERT: C 405 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7505 (mm) REVERT: C 422 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6896 (mmmm) REVERT: C 429 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: C 448 LEU cc_start: 0.7236 (mp) cc_final: 0.6846 (mp) REVERT: C 482 LYS cc_start: 0.7828 (ptpp) cc_final: 0.7320 (mmmt) REVERT: C 584 LEU cc_start: 0.6890 (mt) cc_final: 0.6303 (tp) REVERT: C 590 MET cc_start: 0.5358 (mmp) cc_final: 0.5047 (mmp) REVERT: C 597 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8038 (mt-10) REVERT: D 36 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9161 (tt) REVERT: D 135 ILE cc_start: 0.8776 (tt) cc_final: 0.8412 (mt) REVERT: D 218 ARG cc_start: 0.7327 (ttt180) cc_final: 0.7026 (tmt170) REVERT: D 235 LYS cc_start: 0.7749 (mttt) cc_final: 0.7533 (ptpt) REVERT: D 297 VAL cc_start: 0.8824 (m) cc_final: 0.8581 (p) REVERT: D 353 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6999 (t80) REVERT: D 422 LYS cc_start: 0.7448 (mtpt) cc_final: 0.7229 (mmtt) REVERT: D 426 ASP cc_start: 0.8117 (t0) cc_final: 0.7816 (t0) REVERT: D 446 VAL cc_start: 0.7652 (m) cc_final: 0.6847 (p) REVERT: D 454 GLU cc_start: 0.7273 (tt0) cc_final: 0.6938 (tp30) REVERT: D 467 GLN cc_start: 0.7017 (mt0) cc_final: 0.6671 (tm-30) REVERT: D 571 LYS cc_start: 0.8709 (tttm) cc_final: 0.8447 (ttpt) REVERT: D 592 ASN cc_start: 0.8000 (m-40) cc_final: 0.7270 (t0) REVERT: D 635 PHE cc_start: 0.8416 (m-80) cc_final: 0.8137 (m-80) REVERT: D 686 LYS cc_start: 0.7450 (mttp) cc_final: 0.6915 (mmmm) REVERT: E 46 GLN cc_start: 0.8474 (tp40) cc_final: 0.7805 (tm-30) REVERT: E 99 LEU cc_start: 0.8936 (tp) cc_final: 0.8712 (tp) REVERT: E 112 ASN cc_start: 0.8996 (m-40) cc_final: 0.8653 (m-40) REVERT: E 348 GLU cc_start: 0.6486 (mt-10) cc_final: 0.5545 (pm20) REVERT: E 379 GLN cc_start: 0.7364 (mm110) cc_final: 0.7104 (mm-40) REVERT: F 37 MET cc_start: 0.7919 (ttp) cc_final: 0.7696 (tpp) REVERT: F 44 THR cc_start: 0.8646 (m) cc_final: 0.8246 (p) REVERT: F 156 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4715 (tm-30) REVERT: F 330 TYR cc_start: 0.6203 (t80) cc_final: 0.5799 (t80) REVERT: G 46 GLU cc_start: 0.8802 (tt0) cc_final: 0.8361 (tp30) REVERT: G 56 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7819 (mp0) REVERT: G 104 TYR cc_start: 0.8041 (m-80) cc_final: 0.7430 (m-80) REVERT: H 13 GLN cc_start: 0.6964 (mp10) cc_final: 0.6687 (pp30) REVERT: I 45 ARG cc_start: 0.5653 (ttm110) cc_final: 0.5172 (mtp85) REVERT: I 46 GLU cc_start: 0.8214 (tt0) cc_final: 0.7626 (pm20) REVERT: I 74 ASN cc_start: 0.6239 (m-40) cc_final: 0.5429 (p0) REVERT: I 76 LYS cc_start: 0.7822 (mttm) cc_final: 0.7540 (mptt) REVERT: J 105 TRP cc_start: 0.2574 (m-90) cc_final: 0.2230 (m-10) outliers start: 160 outliers final: 78 residues processed: 552 average time/residue: 0.4307 time to fit residues: 381.4132 Evaluate side-chains 431 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 338 time to evaluate : 3.619 ------------------------------------------------------------------------------- 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 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 295 CYS Chi-restraints excluded: chain A residue 330 ILE 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 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 687 LEU 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 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 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 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL 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 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 40 VAL 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 170 THR Chi-restraints excluded: chain C residue 254 VAL 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 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 730 CYS Chi-restraints excluded: chain D residue 33 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 329 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL 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 619 ILE Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 277 ILE 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 132 LEU Chi-restraints excluded: chain F residue 156 GLU 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 72 ARG Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 78 THR 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 84 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 160 optimal weight: 0.0370 chunk 201 optimal weight: 6.9990 chunk 333 optimal weight: 0.8980 chunk 371 optimal weight: 0.5980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 ASN D 576 ASN ** D 624 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** G 84 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.080423 restraints weight = 79644.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081088 restraints weight = 43774.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081571 restraints weight = 27124.305| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32012 Z= 0.152 Angle : 0.546 10.709 43388 Z= 0.287 Chirality : 0.041 0.171 4903 Planarity : 0.004 0.039 5371 Dihedral : 6.485 72.486 4283 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.81 % Allowed : 12.99 % Favored : 82.20 % 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: -0.32 (0.14), residues: 3759 helix: 0.31 (0.13), residues: 1673 sheet: -0.37 (0.22), residues: 622 loop : -0.59 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 36 HIS 0.011 0.001 HIS J 32 PHE 0.022 0.001 PHE B 682 TYR 0.021 0.001 TYR C 477 ARG 0.005 0.000 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1482) hydrogen bonds : angle 4.53462 ( 3882) SS BOND : bond 0.00451 ( 20) SS BOND : angle 0.92579 ( 40) covalent geometry : bond 0.00342 (31992) covalent geometry : angle 0.54558 (43348) *********************** 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 530 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 363 time to evaluate : 3.303 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: A 104 HIS cc_start: 0.9033 (OUTLIER) cc_final: 0.8316 (t70) REVERT: A 154 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: A 161 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 232 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4445 (mp) REVERT: A 238 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 410 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 415 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7739 (ttpm) REVERT: A 426 ASP cc_start: 0.7039 (t0) cc_final: 0.6809 (t0) REVERT: A 516 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6865 (tptp) REVERT: A 546 LEU cc_start: 0.8313 (tp) cc_final: 0.8070 (tp) REVERT: A 593 LEU cc_start: 0.8638 (tp) cc_final: 0.8432 (tp) REVERT: A 687 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 733 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7596 (mp) REVERT: B 226 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6611 (mmm-85) REVERT: B 244 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: B 410 GLU cc_start: 0.7540 (tp30) cc_final: 0.7209 (tp30) REVERT: B 506 LYS cc_start: 0.8255 (pttm) cc_final: 0.7733 (tmtt) REVERT: B 689 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 806 ASP cc_start: 0.5669 (t70) cc_final: 0.5426 (t70) REVERT: C 243 LEU cc_start: 0.8956 (tp) cc_final: 0.8752 (tp) REVERT: C 348 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7778 (mp) REVERT: C 377 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7319 (m-70) REVERT: C 405 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7540 (mm) REVERT: C 422 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6951 (mmmm) REVERT: C 429 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: C 482 LYS cc_start: 0.7331 (ptpp) cc_final: 0.7042 (mmmt) REVERT: C 584 LEU cc_start: 0.6854 (mt) cc_final: 0.6390 (tp) REVERT: C 590 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5100 (mmp) REVERT: C 635 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: D 135 ILE cc_start: 0.8835 (tt) cc_final: 0.8455 (mt) REVERT: D 218 ARG cc_start: 0.7347 (ttt180) cc_final: 0.7055 (tmt170) REVERT: D 235 LYS cc_start: 0.7770 (mttt) cc_final: 0.7566 (ptpt) REVERT: D 297 VAL cc_start: 0.8800 (m) cc_final: 0.8562 (p) REVERT: D 422 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7251 (mmtt) REVERT: D 434 MET cc_start: 0.7604 (mmm) cc_final: 0.7191 (mmm) REVERT: D 446 VAL cc_start: 0.7662 (m) cc_final: 0.6916 (p) REVERT: D 454 GLU cc_start: 0.7169 (tt0) cc_final: 0.6840 (tp30) REVERT: D 459 VAL cc_start: 0.6938 (OUTLIER) cc_final: 0.6635 (p) REVERT: D 467 GLN cc_start: 0.7059 (mt0) cc_final: 0.6681 (tm-30) REVERT: D 590 MET cc_start: 0.6667 (mpp) cc_final: 0.6406 (mpp) REVERT: D 592 ASN cc_start: 0.7936 (m-40) cc_final: 0.7213 (t0) REVERT: D 635 PHE cc_start: 0.8459 (m-80) cc_final: 0.8002 (m-80) REVERT: D 647 TRP cc_start: 0.7212 (OUTLIER) cc_final: 0.6938 (p90) REVERT: D 686 LYS cc_start: 0.7483 (mttp) cc_final: 0.6932 (mmmm) REVERT: E 46 GLN cc_start: 0.8493 (tp40) cc_final: 0.7820 (tm-30) REVERT: E 48 MET cc_start: 0.7751 (ttt) cc_final: 0.7422 (ttm) REVERT: E 112 ASN cc_start: 0.9099 (m-40) cc_final: 0.8772 (m-40) REVERT: E 117 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 348 GLU cc_start: 0.5407 (mt-10) cc_final: 0.5165 (pm20) REVERT: E 379 GLN cc_start: 0.7402 (mm110) cc_final: 0.7122 (mm-40) REVERT: F 44 THR cc_start: 0.8579 (m) cc_final: 0.8175 (p) REVERT: F 156 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4606 (tm-30) REVERT: F 280 ASN cc_start: 0.7326 (m-40) cc_final: 0.6993 (m110) REVERT: F 300 MET cc_start: 0.8323 (tpp) cc_final: 0.8021 (mmp) REVERT: F 330 TYR cc_start: 0.6087 (t80) cc_final: 0.5780 (t80) REVERT: G 46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8433 (tp30) REVERT: G 56 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7805 (mp0) REVERT: G 104 TYR cc_start: 0.8070 (m-80) cc_final: 0.7561 (m-80) REVERT: H 13 GLN cc_start: 0.6911 (mp10) cc_final: 0.6659 (pp30) REVERT: I 3 GLN cc_start: 0.5779 (pp30) cc_final: 0.4993 (pp30) REVERT: I 74 ASN cc_start: 0.6057 (m-40) cc_final: 0.5029 (p0) REVERT: I 76 LYS cc_start: 0.7772 (mttm) cc_final: 0.7508 (mptt) REVERT: J 32 HIS cc_start: 0.6499 (m90) cc_final: 0.6295 (m-70) REVERT: J 36 TRP cc_start: 0.5934 (m100) cc_final: 0.4931 (m100) REVERT: J 51 ILE cc_start: 0.2607 (tp) cc_final: 0.1508 (mm) REVERT: J 105 TRP cc_start: 0.2659 (m-90) cc_final: 0.2304 (m-10) outliers start: 167 outliers final: 101 residues processed: 496 average time/residue: 0.4229 time to fit residues: 340.9705 Evaluate side-chains 441 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 320 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 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 161 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 279 ILE 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 410 GLU Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU 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 647 TRP Chi-restraints excluded: chain A residue 687 LEU 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 B residue 60 VAL 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 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 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 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 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 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 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 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 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 407 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 767 GLU 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 257 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 339 TYR 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 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 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 29 VAL 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 64 optimal weight: 1.9990 chunk 323 optimal weight: 0.0370 chunk 294 optimal weight: 0.6980 chunk 339 optimal weight: 6.9990 chunk 70 optimal weight: 0.0060 chunk 317 optimal weight: 0.0010 chunk 264 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.3480 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS C 636 GLN D 431 HIS D 615 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.119210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080441 restraints weight = 79086.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082097 restraints weight = 41488.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082782 restraints weight = 25451.882| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 32012 Z= 0.104 Angle : 0.504 9.307 43388 Z= 0.264 Chirality : 0.040 0.145 4903 Planarity : 0.003 0.037 5371 Dihedral : 6.049 70.155 4264 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.03 % Allowed : 14.60 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3759 helix: 0.34 (0.13), residues: 1710 sheet: -0.32 (0.22), residues: 622 loop : -0.64 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 145 HIS 0.006 0.001 HIS J 32 PHE 0.023 0.001 PHE F 41 TYR 0.027 0.001 TYR C 477 ARG 0.007 0.000 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1482) hydrogen bonds : angle 4.30674 ( 3882) SS BOND : bond 0.00335 ( 20) SS BOND : angle 0.83427 ( 40) covalent geometry : bond 0.00224 (31992) covalent geometry : angle 0.50374 (43348) *********************** 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 511 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 371 time to evaluate : 3.357 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: 0.8972 (OUTLIER) cc_final: 0.8232 (t70) REVERT: A 154 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: A 161 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8244 (pp) REVERT: A 238 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 426 ASP cc_start: 0.7110 (t0) cc_final: 0.6882 (t0) REVERT: A 516 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6810 (tptp) REVERT: A 546 LEU cc_start: 0.8289 (tp) cc_final: 0.8045 (tp) REVERT: A 687 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 733 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 226 ARG cc_start: 0.6996 (mtp85) cc_final: 0.6571 (mmm-85) REVERT: B 244 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.5420 (m-80) REVERT: B 410 GLU cc_start: 0.7480 (tp30) cc_final: 0.7186 (tp30) REVERT: B 448 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (tp) REVERT: B 506 LYS cc_start: 0.8168 (pttm) cc_final: 0.7748 (tmtt) REVERT: B 689 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 721 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6402 (pt0) REVERT: C 110 ASP cc_start: 0.8133 (m-30) cc_final: 0.7865 (t0) REVERT: C 243 LEU cc_start: 0.8990 (tp) cc_final: 0.8703 (tp) REVERT: C 348 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7964 (mp) REVERT: C 377 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7261 (m-70) REVERT: C 405 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7444 (mm) REVERT: C 422 LYS cc_start: 0.7181 (mtpt) cc_final: 0.6653 (mmmm) REVERT: C 429 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: C 482 LYS cc_start: 0.7327 (ptpp) cc_final: 0.7054 (tttt) REVERT: C 590 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5414 (mmp) REVERT: C 688 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: D 135 ILE cc_start: 0.8769 (tt) cc_final: 0.8383 (mt) REVERT: D 218 ARG cc_start: 0.7232 (ttt180) cc_final: 0.7014 (tmt170) REVERT: D 235 LYS cc_start: 0.7778 (mttt) cc_final: 0.7569 (ptpt) REVERT: D 297 VAL cc_start: 0.8707 (m) cc_final: 0.8470 (p) REVERT: D 434 MET cc_start: 0.7654 (mmm) cc_final: 0.7212 (mmm) REVERT: D 446 VAL cc_start: 0.7727 (m) cc_final: 0.6982 (p) REVERT: D 454 GLU cc_start: 0.7124 (tt0) cc_final: 0.6816 (tp30) REVERT: D 467 GLN cc_start: 0.6993 (mt0) cc_final: 0.6670 (tm-30) REVERT: D 555 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6431 (mt) REVERT: D 590 MET cc_start: 0.7504 (mpp) cc_final: 0.7282 (mpp) REVERT: D 592 ASN cc_start: 0.7950 (m-40) cc_final: 0.7386 (t0) REVERT: D 647 TRP cc_start: 0.7232 (OUTLIER) cc_final: 0.6982 (p90) REVERT: D 686 LYS cc_start: 0.7486 (mttp) cc_final: 0.6964 (mmmm) REVERT: E 46 GLN cc_start: 0.8439 (tp40) cc_final: 0.7822 (tm-30) REVERT: E 99 LEU cc_start: 0.8866 (tp) cc_final: 0.8477 (tt) REVERT: E 112 ASN cc_start: 0.8914 (m-40) cc_final: 0.8628 (m-40) REVERT: E 348 GLU cc_start: 0.5378 (mt-10) cc_final: 0.5177 (pm20) REVERT: E 379 GLN cc_start: 0.7377 (mm110) cc_final: 0.7159 (mm-40) REVERT: F 44 THR cc_start: 0.8475 (m) cc_final: 0.8108 (p) REVERT: F 114 MET cc_start: 0.8674 (tpp) cc_final: 0.8082 (tpp) REVERT: F 276 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.6147 (mm) REVERT: F 280 ASN cc_start: 0.7253 (m-40) cc_final: 0.6868 (m110) REVERT: F 300 MET cc_start: 0.8274 (tpp) cc_final: 0.7936 (mmp) REVERT: F 318 LYS cc_start: 0.7292 (tppt) cc_final: 0.7056 (tppt) REVERT: G 43 LYS cc_start: 0.6889 (mtmt) cc_final: 0.6644 (pttt) REVERT: G 46 GLU cc_start: 0.8858 (tt0) cc_final: 0.8405 (tp30) REVERT: G 56 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7759 (mp0) REVERT: G 83 MET cc_start: 0.7121 (mtm) cc_final: 0.6583 (mpp) REVERT: H 13 GLN cc_start: 0.6980 (mp10) cc_final: 0.6755 (pp30) REVERT: H 34 MET cc_start: 0.7372 (mmm) cc_final: 0.7133 (mmt) REVERT: H 38 ARG cc_start: 0.7630 (ptt180) cc_final: 0.7399 (ptm160) REVERT: I 3 GLN cc_start: 0.5631 (OUTLIER) cc_final: 0.4890 (pp30) REVERT: I 74 ASN cc_start: 0.5980 (m-40) cc_final: 0.4994 (p0) REVERT: J 31 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7060 (tpt90) REVERT: J 36 TRP cc_start: 0.5784 (m100) cc_final: 0.4857 (m100) REVERT: J 51 ILE cc_start: 0.2675 (tp) cc_final: 0.1844 (mm) REVERT: J 95 TYR cc_start: 0.6193 (m-80) cc_final: 0.5721 (m-80) REVERT: J 105 TRP cc_start: 0.2555 (m-90) cc_final: 0.2227 (m-10) outliers start: 140 outliers final: 80 residues processed: 484 average time/residue: 0.4084 time to fit residues: 322.0085 Evaluate side-chains 425 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 326 time to evaluate : 3.554 ------------------------------------------------------------------------------- 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 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 295 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 MET 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 516 LYS 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 687 LEU 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 733 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 161 LEU 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 292 ASP Chi-restraints excluded: chain B residue 299 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 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 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 47 VAL Chi-restraints excluded: chain C residue 60 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 303 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 565 VAL Chi-restraints excluded: chain C residue 590 MET 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 33 ILE 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 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 38 ILE 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 132 LEU Chi-restraints excluded: chain F residue 276 ILE 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 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 78 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 365 optimal weight: 5.9990 chunk 347 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 375 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 75 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN C 636 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN G 110 GLN I 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.116839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079589 restraints weight = 79307.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079919 restraints weight = 49592.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079847 restraints weight = 33604.401| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32012 Z= 0.163 Angle : 0.541 8.847 43388 Z= 0.282 Chirality : 0.041 0.154 4903 Planarity : 0.004 0.051 5371 Dihedral : 5.819 71.877 4252 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.58 % Allowed : 15.26 % Favored : 80.16 % 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: -0.33 (0.14), residues: 3759 helix: 0.29 (0.13), residues: 1705 sheet: -0.40 (0.22), residues: 626 loop : -0.58 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 340 HIS 0.006 0.001 HIS F 134 PHE 0.019 0.001 PHE C 353 TYR 0.024 0.001 TYR D 325 ARG 0.005 0.000 ARG J 72 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1482) hydrogen bonds : angle 4.34317 ( 3882) SS BOND : bond 0.00402 ( 20) SS BOND : angle 0.80333 ( 40) covalent geometry : bond 0.00373 (31992) covalent geometry : angle 0.54029 (43348) *********************** 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 493 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 334 time to evaluate : 3.667 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: 0.9091 (OUTLIER) cc_final: 0.8444 (t70) REVERT: A 154 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: A 161 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 238 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 415 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7920 (ttpm) REVERT: A 426 ASP cc_start: 0.7298 (t0) cc_final: 0.7068 (t0) REVERT: A 516 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6773 (tptp) REVERT: A 546 LEU cc_start: 0.8329 (tp) cc_final: 0.8108 (tp) REVERT: A 626 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8903 (mm) REVERT: A 687 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8399 (mt) REVERT: A 733 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 226 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6578 (mmm-85) REVERT: B 244 PHE cc_start: 0.6633 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: B 350 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5415 (ttpp) REVERT: B 410 GLU cc_start: 0.7498 (tp30) cc_final: 0.7229 (tp30) REVERT: B 444 ASP cc_start: 0.7722 (t70) cc_final: 0.7405 (t0) REVERT: B 448 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8683 (tt) REVERT: B 506 LYS cc_start: 0.8383 (pttm) cc_final: 0.7777 (tmtt) REVERT: B 689 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: B 721 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: C 243 LEU cc_start: 0.9012 (tp) cc_final: 0.8650 (tp) REVERT: C 377 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7332 (m-70) REVERT: C 405 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7429 (mm) REVERT: C 422 LYS cc_start: 0.7274 (mtpt) cc_final: 0.6895 (mmmm) REVERT: C 590 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5485 (mmp) REVERT: C 597 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7818 (mp0) REVERT: C 688 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7596 (mtm180) REVERT: D 135 ILE cc_start: 0.8861 (tt) cc_final: 0.8479 (mt) REVERT: D 218 ARG cc_start: 0.7348 (ttt180) cc_final: 0.7027 (tmt170) REVERT: D 297 VAL cc_start: 0.8777 (m) cc_final: 0.8562 (p) REVERT: D 434 MET cc_start: 0.7755 (mmm) cc_final: 0.7316 (mmm) REVERT: D 446 VAL cc_start: 0.7833 (m) cc_final: 0.7071 (p) REVERT: D 454 GLU cc_start: 0.7268 (tt0) cc_final: 0.6848 (tp30) REVERT: D 459 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6638 (p) REVERT: D 467 GLN cc_start: 0.7094 (mt0) cc_final: 0.6686 (tm-30) REVERT: D 555 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6266 (mt) REVERT: D 590 MET cc_start: 0.7563 (mpp) cc_final: 0.7327 (mpp) REVERT: D 592 ASN cc_start: 0.7957 (m-40) cc_final: 0.7332 (t0) REVERT: D 686 LYS cc_start: 0.7473 (mttp) cc_final: 0.6870 (mmmm) REVERT: E 46 GLN cc_start: 0.8538 (tp40) cc_final: 0.7795 (tm-30) REVERT: E 112 ASN cc_start: 0.9017 (m-40) cc_final: 0.8793 (m110) REVERT: E 113 GLN cc_start: 0.7508 (mt0) cc_final: 0.6430 (mt0) REVERT: E 145 TRP cc_start: 0.5236 (t60) cc_final: 0.4620 (t60) REVERT: E 248 PHE cc_start: 0.6851 (t80) cc_final: 0.6529 (t80) REVERT: E 348 GLU cc_start: 0.5357 (mt-10) cc_final: 0.5092 (pm20) REVERT: F 44 THR cc_start: 0.8492 (m) cc_final: 0.8089 (p) REVERT: F 276 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6152 (mm) REVERT: F 280 ASN cc_start: 0.7225 (m-40) cc_final: 0.6837 (m110) REVERT: F 300 MET cc_start: 0.8335 (tpp) cc_final: 0.7991 (mmp) REVERT: F 330 TYR cc_start: 0.6050 (t80) cc_final: 0.5732 (t80) REVERT: G 46 GLU cc_start: 0.8885 (tt0) cc_final: 0.8454 (tp30) REVERT: G 56 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7803 (mp0) REVERT: G 83 MET cc_start: 0.6937 (mtm) cc_final: 0.5920 (mpp) REVERT: H 13 GLN cc_start: 0.7028 (mp10) cc_final: 0.6782 (pp30) REVERT: I 74 ASN cc_start: 0.6051 (m-40) cc_final: 0.4970 (p0) REVERT: J 36 TRP cc_start: 0.5642 (m100) cc_final: 0.4787 (m100) REVERT: J 51 ILE cc_start: 0.2652 (tp) cc_final: 0.1999 (mm) REVERT: J 95 TYR cc_start: 0.6270 (m-80) cc_final: 0.5719 (m-80) outliers start: 159 outliers final: 112 residues processed: 464 average time/residue: 0.4225 time to fit residues: 320.3628 Evaluate side-chains 436 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 305 time to evaluate : 3.509 ------------------------------------------------------------------------------- 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 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 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 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 536 VAL 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 687 LEU 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 778 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 VAL 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 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 392 VAL 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 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 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 157 VAL Chi-restraints excluded: chain C residue 159 ILE 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 303 THR 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 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 33 ILE 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 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 368 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 555 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 650 HIS 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 47 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 31 LEU 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 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 276 ILE 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 29 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 131 optimal weight: 0.0370 chunk 180 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 295 optimal weight: 2.9990 chunk 244 optimal weight: 0.0060 chunk 307 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 345 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.3874 ------------------------------------------------------------------------------- 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 660 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN D 712 ASN F 113 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.118307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080335 restraints weight = 78701.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.081762 restraints weight = 44322.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081701 restraints weight = 27972.106| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 32012 Z= 0.103 Angle : 0.503 8.394 43388 Z= 0.263 Chirality : 0.040 0.158 4903 Planarity : 0.003 0.041 5371 Dihedral : 5.666 69.384 4252 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.92 % Allowed : 15.90 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3759 helix: 0.40 (0.13), residues: 1710 sheet: -0.25 (0.21), residues: 646 loop : -0.58 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 647 HIS 0.005 0.001 HIS F 134 PHE 0.024 0.001 PHE F 41 TYR 0.025 0.001 TYR D 325 ARG 0.007 0.000 ARG F 118 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1482) hydrogen bonds : angle 4.17588 ( 3882) SS BOND : bond 0.00324 ( 20) SS BOND : angle 0.73014 ( 40) covalent geometry : bond 0.00227 (31992) covalent geometry : angle 0.50273 (43348) *********************** 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 488 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 352 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8992 (OUTLIER) cc_final: 0.8193 (t70) REVERT: A 154 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: A 161 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8216 (pp) REVERT: A 238 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 426 ASP cc_start: 0.7258 (t0) cc_final: 0.7035 (t0) REVERT: A 516 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6753 (tptp) REVERT: A 626 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8852 (mm) REVERT: A 687 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 733 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7676 (mp) REVERT: B 226 ARG cc_start: 0.6987 (mtp85) cc_final: 0.6543 (mmm-85) REVERT: B 244 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5437 (m-80) REVERT: B 410 GLU cc_start: 0.7428 (tp30) cc_final: 0.7189 (tp30) REVERT: B 444 ASP cc_start: 0.7755 (t70) cc_final: 0.7411 (t0) REVERT: B 506 LYS cc_start: 0.8371 (pttm) cc_final: 0.7782 (tmtt) REVERT: B 590 MET cc_start: 0.8441 (mmm) cc_final: 0.8015 (mmm) REVERT: B 689 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7598 (m-80) REVERT: B 721 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6402 (pt0) REVERT: C 243 LEU cc_start: 0.8970 (tp) cc_final: 0.8658 (tp) REVERT: C 353 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.6202 (t80) REVERT: C 377 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6931 (m170) REVERT: C 405 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7400 (mm) REVERT: C 422 LYS cc_start: 0.7228 (mtpt) cc_final: 0.6792 (mmmm) REVERT: C 429 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6486 (pm20) REVERT: C 590 MET cc_start: 0.5978 (mmp) cc_final: 0.5685 (mmp) REVERT: C 688 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7482 (mtm-85) REVERT: D 135 ILE cc_start: 0.8792 (tt) cc_final: 0.8368 (mt) REVERT: D 218 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6962 (tmt170) REVERT: D 297 VAL cc_start: 0.8740 (m) cc_final: 0.8523 (p) REVERT: D 434 MET cc_start: 0.7830 (mmm) cc_final: 0.7355 (mmm) REVERT: D 446 VAL cc_start: 0.7760 (m) cc_final: 0.6978 (p) REVERT: D 454 GLU cc_start: 0.7209 (tt0) cc_final: 0.6829 (tp30) REVERT: D 459 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6432 (p) REVERT: D 467 GLN cc_start: 0.7032 (mt0) cc_final: 0.6673 (tm-30) REVERT: D 555 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6204 (mt) REVERT: D 590 MET cc_start: 0.7522 (mpp) cc_final: 0.7284 (mpp) REVERT: D 592 ASN cc_start: 0.7918 (m-40) cc_final: 0.7331 (t0) REVERT: D 686 LYS cc_start: 0.7394 (mttp) cc_final: 0.6792 (mmmm) REVERT: E 46 GLN cc_start: 0.8482 (tp40) cc_final: 0.7818 (tm-30) REVERT: E 99 LEU cc_start: 0.8862 (tp) cc_final: 0.8445 (tt) REVERT: E 145 TRP cc_start: 0.5196 (t60) cc_final: 0.4804 (t60) REVERT: E 248 PHE cc_start: 0.6832 (t80) cc_final: 0.6522 (t80) REVERT: E 348 GLU cc_start: 0.5372 (mt-10) cc_final: 0.5095 (pm20) REVERT: F 44 THR cc_start: 0.8422 (m) cc_final: 0.8023 (p) REVERT: F 276 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.6108 (mm) REVERT: F 280 ASN cc_start: 0.6884 (m-40) cc_final: 0.6480 (m110) REVERT: F 300 MET cc_start: 0.8293 (tpp) cc_final: 0.7929 (mmp) REVERT: F 330 TYR cc_start: 0.5836 (t80) cc_final: 0.5532 (t80) REVERT: G 46 GLU cc_start: 0.8883 (tt0) cc_final: 0.8443 (tp30) REVERT: G 56 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7760 (mp0) REVERT: G 83 MET cc_start: 0.6847 (mtm) cc_final: 0.5702 (mpp) REVERT: G 107 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6179 (pm20) REVERT: H 13 GLN cc_start: 0.7115 (mp10) cc_final: 0.6879 (pp30) REVERT: H 34 MET cc_start: 0.7400 (mmm) cc_final: 0.7160 (mmt) REVERT: I 32 HIS cc_start: 0.5357 (OUTLIER) cc_final: 0.3985 (m-70) REVERT: I 74 ASN cc_start: 0.6017 (m-40) cc_final: 0.4960 (p0) REVERT: J 36 TRP cc_start: 0.5709 (m100) cc_final: 0.5305 (m100) outliers start: 136 outliers final: 86 residues processed: 464 average time/residue: 0.4122 time to fit residues: 312.0809 Evaluate side-chains 423 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 319 time to evaluate : 3.345 ------------------------------------------------------------------------------- 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 97 ILE 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 279 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 343 MET 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 516 LYS 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 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 687 LEU 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 733 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL 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 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 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 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 159 ILE 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 303 THR 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 537 ILE Chi-restraints excluded: chain C residue 565 VAL 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 33 ILE 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 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 407 LEU 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 555 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 151 SER 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 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 276 ILE 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 H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 32 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 247 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 362 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 304 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.117044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.078645 restraints weight = 79646.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080066 restraints weight = 46379.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080243 restraints weight = 28225.509| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 32012 Z= 0.158 Angle : 0.532 9.946 43388 Z= 0.277 Chirality : 0.041 0.230 4903 Planarity : 0.003 0.058 5371 Dihedral : 5.680 71.268 4244 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.23 % Allowed : 16.19 % Favored : 79.58 % 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: 0.38 (0.13), residues: 1706 sheet: -0.30 (0.21), residues: 646 loop : -0.59 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 36 HIS 0.009 0.001 HIS D 119 PHE 0.054 0.001 PHE D 611 TYR 0.039 0.001 TYR D 325 ARG 0.007 0.000 ARG I 67 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 1482) hydrogen bonds : angle 4.23437 ( 3882) SS BOND : bond 0.00394 ( 20) SS BOND : angle 0.87166 ( 40) covalent geometry : bond 0.00364 (31992) covalent geometry : angle 0.53120 (43348) *********************** 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 468 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 321 time to evaluate : 3.442 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: 0.9082 (OUTLIER) cc_final: 0.8362 (t70) REVERT: A 154 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 161 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 238 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 426 ASP cc_start: 0.7340 (t0) cc_final: 0.7110 (t0) REVERT: A 516 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6963 (tptp) REVERT: A 626 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8841 (mm) REVERT: A 687 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8395 (mt) REVERT: A 733 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 226 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6561 (mmm-85) REVERT: B 244 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.5544 (m-80) REVERT: B 350 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5461 (ttpp) REVERT: B 410 GLU cc_start: 0.7503 (tp30) cc_final: 0.7247 (tp30) REVERT: B 444 ASP cc_start: 0.7910 (t70) cc_final: 0.7579 (t0) REVERT: B 448 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8706 (tp) REVERT: B 506 LYS cc_start: 0.8394 (pttm) cc_final: 0.7795 (tmtt) REVERT: B 590 MET cc_start: 0.8476 (mmm) cc_final: 0.8043 (mmm) REVERT: B 689 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: B 721 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6422 (pt0) REVERT: C 243 LEU cc_start: 0.9016 (tp) cc_final: 0.8667 (tp) REVERT: C 353 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6553 (t80) REVERT: C 377 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.6991 (m170) REVERT: C 405 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7469 (mm) REVERT: C 422 LYS cc_start: 0.7284 (mtpt) cc_final: 0.6890 (mmmm) REVERT: C 590 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5696 (mmp) REVERT: C 635 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: C 688 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: D 135 ILE cc_start: 0.8872 (tt) cc_final: 0.8500 (mt) REVERT: D 218 ARG cc_start: 0.7264 (ttt180) cc_final: 0.6970 (tmt170) REVERT: D 297 VAL cc_start: 0.8782 (m) cc_final: 0.8563 (p) REVERT: D 434 MET cc_start: 0.7846 (mmm) cc_final: 0.7350 (mmm) REVERT: D 446 VAL cc_start: 0.7771 (m) cc_final: 0.6994 (p) REVERT: D 454 GLU cc_start: 0.7352 (tt0) cc_final: 0.6928 (tp30) REVERT: D 459 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6741 (p) REVERT: D 467 GLN cc_start: 0.7101 (mt0) cc_final: 0.6679 (tm-30) REVERT: D 555 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6280 (mt) REVERT: D 590 MET cc_start: 0.7478 (mpp) cc_final: 0.7226 (mpp) REVERT: D 592 ASN cc_start: 0.7976 (m-40) cc_final: 0.7356 (t0) REVERT: D 686 LYS cc_start: 0.7522 (mttp) cc_final: 0.6865 (mmmm) REVERT: E 46 GLN cc_start: 0.8551 (tp40) cc_final: 0.7802 (tm-30) REVERT: E 117 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7736 (tm-30) REVERT: E 145 TRP cc_start: 0.5324 (t60) cc_final: 0.4883 (t60) REVERT: E 248 PHE cc_start: 0.6706 (t80) cc_final: 0.6370 (t80) REVERT: E 348 GLU cc_start: 0.5221 (mt-10) cc_final: 0.4970 (pm20) REVERT: F 44 THR cc_start: 0.8422 (m) cc_final: 0.8024 (p) REVERT: F 114 MET cc_start: 0.8867 (mmm) cc_final: 0.8405 (tpt) REVERT: F 276 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.6062 (mm) REVERT: F 280 ASN cc_start: 0.6899 (m-40) cc_final: 0.6461 (m110) REVERT: F 300 MET cc_start: 0.8364 (tpp) cc_final: 0.7963 (mmp) REVERT: F 330 TYR cc_start: 0.5904 (t80) cc_final: 0.5650 (t80) REVERT: G 46 GLU cc_start: 0.8871 (tt0) cc_final: 0.8431 (tp30) REVERT: G 56 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7762 (mp0) REVERT: G 83 MET cc_start: 0.6975 (mtm) cc_final: 0.5735 (mpp) REVERT: H 27 PHE cc_start: 0.6016 (p90) cc_final: 0.5440 (p90) REVERT: H 34 MET cc_start: 0.7441 (mmm) cc_final: 0.7157 (mmt) REVERT: I 74 ASN cc_start: 0.6043 (m-40) cc_final: 0.5004 (p0) REVERT: J 36 TRP cc_start: 0.5724 (m100) cc_final: 0.5501 (m100) REVERT: J 72 ARG cc_start: 0.4027 (ptt180) cc_final: 0.3746 (ptt180) outliers start: 147 outliers final: 108 residues processed: 440 average time/residue: 0.3931 time to fit residues: 286.8064 Evaluate side-chains 435 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 307 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 97 ILE 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 279 ILE Chi-restraints excluded: chain A residue 314 LEU 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 516 LYS 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 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 687 LEU 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 733 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL 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 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 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 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 155 HIS Chi-restraints excluded: chain C residue 159 ILE 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 303 THR 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 635 PHE Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 757 THR 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 161 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 ARG 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 368 VAL Chi-restraints excluded: chain D residue 407 LEU 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 555 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 626 LEU Chi-restraints excluded: chain D residue 650 HIS 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 151 SER 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 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU 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 276 ILE 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 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 324 optimal weight: 4.9990 chunk 293 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 338 optimal weight: 0.0870 chunk 254 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078304 restraints weight = 79726.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.079884 restraints weight = 44594.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080108 restraints weight = 27266.205| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32012 Z= 0.154 Angle : 0.537 9.538 43388 Z= 0.280 Chirality : 0.041 0.204 4903 Planarity : 0.003 0.040 5371 Dihedral : 5.696 71.261 4241 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.35 % Allowed : 16.76 % Favored : 78.89 % 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: -0.21 (0.14), residues: 3759 helix: 0.45 (0.13), residues: 1672 sheet: -0.37 (0.22), residues: 616 loop : -0.57 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 340 HIS 0.007 0.001 HIS D 104 PHE 0.034 0.001 PHE D 611 TYR 0.042 0.001 TYR D 325 ARG 0.007 0.000 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 1482) hydrogen bonds : angle 4.25218 ( 3882) SS BOND : bond 0.00371 ( 20) SS BOND : angle 0.77653 ( 40) covalent geometry : bond 0.00353 (31992) covalent geometry : angle 0.53685 (43348) *********************** 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 471 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 320 time to evaluate : 6.172 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: 0.9029 (OUTLIER) cc_final: 0.8261 (t70) REVERT: A 154 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: A 161 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8242 (pp) REVERT: A 238 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 426 ASP cc_start: 0.7344 (t0) cc_final: 0.7117 (t0) REVERT: A 516 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6991 (tptp) REVERT: A 626 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8837 (mm) REVERT: A 687 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 708 GLN cc_start: 0.7216 (mm110) cc_final: 0.6765 (mp10) REVERT: A 733 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7570 (mp) REVERT: B 226 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6575 (mmm-85) REVERT: B 244 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.5702 (m-80) REVERT: B 337 MET cc_start: 0.7349 (ppp) cc_final: 0.7112 (ppp) REVERT: B 350 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5476 (ttpp) REVERT: B 410 GLU cc_start: 0.7521 (tp30) cc_final: 0.7272 (tp30) REVERT: B 444 ASP cc_start: 0.7928 (t70) cc_final: 0.7606 (t0) REVERT: B 448 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 506 LYS cc_start: 0.8375 (pttm) cc_final: 0.7797 (tmtt) REVERT: B 590 MET cc_start: 0.8468 (mmm) cc_final: 0.8011 (mmm) REVERT: B 689 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7654 (m-80) REVERT: B 721 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: C 243 LEU cc_start: 0.9047 (tp) cc_final: 0.8732 (tp) REVERT: C 353 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6620 (t80) REVERT: C 377 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7007 (m170) REVERT: C 405 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7488 (mm) REVERT: C 422 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6887 (mmmm) REVERT: C 429 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: C 590 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5722 (mmp) REVERT: C 635 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7051 (m-10) REVERT: C 644 LEU cc_start: 0.6337 (tp) cc_final: 0.6134 (tp) REVERT: C 688 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: D 135 ILE cc_start: 0.8862 (tt) cc_final: 0.8483 (mt) REVERT: D 218 ARG cc_start: 0.7271 (ttt180) cc_final: 0.6970 (tmt170) REVERT: D 434 MET cc_start: 0.7844 (mmm) cc_final: 0.7345 (mmm) REVERT: D 446 VAL cc_start: 0.7887 (m) cc_final: 0.7190 (p) REVERT: D 454 GLU cc_start: 0.7405 (tt0) cc_final: 0.6978 (tp30) REVERT: D 459 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6741 (p) REVERT: D 467 GLN cc_start: 0.7114 (mt0) cc_final: 0.6724 (tm-30) REVERT: D 587 LEU cc_start: 0.8777 (mm) cc_final: 0.8521 (mm) REVERT: D 590 MET cc_start: 0.7493 (mpp) cc_final: 0.7243 (mpp) REVERT: D 592 ASN cc_start: 0.7996 (m-40) cc_final: 0.7381 (t0) REVERT: D 686 LYS cc_start: 0.7696 (mttp) cc_final: 0.6988 (mmmm) REVERT: E 46 GLN cc_start: 0.8560 (tp40) cc_final: 0.8204 (tp40) REVERT: E 49 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7077 (mm-40) REVERT: E 113 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: E 145 TRP cc_start: 0.5479 (t60) cc_final: 0.5081 (t60) REVERT: E 248 PHE cc_start: 0.6801 (t80) cc_final: 0.6388 (t80) REVERT: E 348 GLU cc_start: 0.5410 (mt-10) cc_final: 0.5098 (pm20) REVERT: F 44 THR cc_start: 0.8440 (m) cc_final: 0.8043 (p) REVERT: F 118 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7784 (mmt90) REVERT: F 156 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.5081 (tm-30) REVERT: F 280 ASN cc_start: 0.6946 (m-40) cc_final: 0.6499 (m110) REVERT: F 330 TYR cc_start: 0.5853 (t80) cc_final: 0.5631 (t80) REVERT: G 46 GLU cc_start: 0.8842 (tt0) cc_final: 0.8409 (tp30) REVERT: G 56 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7743 (mp0) REVERT: G 83 MET cc_start: 0.7056 (mtm) cc_final: 0.5806 (mpp) REVERT: H 27 PHE cc_start: 0.5893 (p90) cc_final: 0.5506 (p90) REVERT: H 68 PHE cc_start: 0.8133 (m-10) cc_final: 0.7381 (m-10) REVERT: I 32 HIS cc_start: 0.5913 (OUTLIER) cc_final: 0.4643 (m-70) REVERT: I 74 ASN cc_start: 0.6044 (m-40) cc_final: 0.4999 (p0) outliers start: 151 outliers final: 116 residues processed: 442 average time/residue: 0.4265 time to fit residues: 314.5126 Evaluate side-chains 446 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 308 time to evaluate : 3.987 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain A residue 97 ILE 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 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 314 LEU 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 516 LYS 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 626 LEU Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 687 LEU 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 757 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL 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 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 396 GLU 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 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 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 155 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 159 ILE 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 303 THR 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 757 THR 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 161 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 ARG 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 368 VAL Chi-restraints excluded: chain D residue 407 LEU 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 626 LEU Chi-restraints excluded: chain D residue 650 HIS 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 47 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 151 SER 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 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU 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 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 G residue 69 THR 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 32 HIS 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 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 277 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** F 134 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.117979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079637 restraints weight = 79072.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081372 restraints weight = 43968.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081407 restraints weight = 26409.404| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 32012 Z= 0.110 Angle : 0.511 9.492 43388 Z= 0.265 Chirality : 0.040 0.202 4903 Planarity : 0.003 0.040 5371 Dihedral : 5.605 69.687 4241 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.83 % Allowed : 17.37 % Favored : 78.80 % 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: -0.13 (0.14), residues: 3759 helix: 0.52 (0.13), residues: 1676 sheet: -0.37 (0.22), residues: 616 loop : -0.50 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 36 HIS 0.006 0.001 HIS D 104 PHE 0.032 0.001 PHE D 611 TYR 0.041 0.001 TYR D 325 ARG 0.010 0.000 ARG J 72 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 1482) hydrogen bonds : angle 4.14039 ( 3882) SS BOND : bond 0.00302 ( 20) SS BOND : angle 0.75718 ( 40) covalent geometry : bond 0.00247 (31992) covalent geometry : angle 0.51109 (43348) *********************** 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 468 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 335 time to evaluate : 3.343 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: 0.8990 (OUTLIER) cc_final: 0.8154 (t70) REVERT: A 154 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: A 161 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (pp) REVERT: A 238 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8070 (mm-30) REVERT: A 426 ASP cc_start: 0.7345 (t0) cc_final: 0.7127 (t0) REVERT: A 516 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6973 (tptp) REVERT: A 687 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 708 GLN cc_start: 0.7075 (mm110) cc_final: 0.6651 (mp10) REVERT: A 733 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7683 (mp) REVERT: B 226 ARG cc_start: 0.6967 (mtp85) cc_final: 0.6522 (mmm-85) REVERT: B 244 PHE cc_start: 0.6662 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: B 337 MET cc_start: 0.7470 (ppp) cc_final: 0.7263 (ppp) REVERT: B 410 GLU cc_start: 0.7472 (tp30) cc_final: 0.7252 (tp30) REVERT: B 434 MET cc_start: 0.7111 (mmp) cc_final: 0.6390 (ttp) REVERT: B 444 ASP cc_start: 0.7874 (t70) cc_final: 0.7559 (t0) REVERT: B 448 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 506 LYS cc_start: 0.8386 (pttm) cc_final: 0.7799 (tmtt) REVERT: B 590 MET cc_start: 0.8448 (mmm) cc_final: 0.7978 (mmm) REVERT: B 689 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7642 (m-80) REVERT: B 721 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: C 243 LEU cc_start: 0.9042 (tp) cc_final: 0.8731 (tp) REVERT: C 353 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6617 (t80) REVERT: C 377 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.6912 (m170) REVERT: C 405 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7482 (mm) REVERT: C 422 LYS cc_start: 0.7278 (mtpt) cc_final: 0.6873 (mmmm) REVERT: C 590 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.6010 (mmp) REVERT: C 688 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: D 135 ILE cc_start: 0.8814 (tt) cc_final: 0.8416 (mt) REVERT: D 218 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6943 (tmt170) REVERT: D 434 MET cc_start: 0.7848 (mmm) cc_final: 0.7336 (mmm) REVERT: D 446 VAL cc_start: 0.7936 (m) cc_final: 0.7251 (p) REVERT: D 454 GLU cc_start: 0.7362 (tt0) cc_final: 0.6922 (tp30) REVERT: D 459 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6715 (p) REVERT: D 467 GLN cc_start: 0.7064 (mt0) cc_final: 0.6717 (tm-30) REVERT: D 587 LEU cc_start: 0.8766 (mm) cc_final: 0.8506 (mm) REVERT: D 590 MET cc_start: 0.7543 (mpp) cc_final: 0.7273 (mpp) REVERT: D 592 ASN cc_start: 0.7994 (m-40) cc_final: 0.7381 (t0) REVERT: D 686 LYS cc_start: 0.7688 (mttp) cc_final: 0.6988 (mmmm) REVERT: E 46 GLN cc_start: 0.8509 (tp40) cc_final: 0.7807 (tm-30) REVERT: E 49 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7184 (mm-40) REVERT: E 113 GLN cc_start: 0.7772 (mt0) cc_final: 0.7391 (mt0) REVERT: E 145 TRP cc_start: 0.5586 (t60) cc_final: 0.5351 (t60) REVERT: E 248 PHE cc_start: 0.6974 (t80) cc_final: 0.6450 (t80) REVERT: E 348 GLU cc_start: 0.5540 (mt-10) cc_final: 0.5206 (pm20) REVERT: F 44 THR cc_start: 0.8412 (m) cc_final: 0.8027 (p) REVERT: F 156 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5240 (tm-30) REVERT: F 280 ASN cc_start: 0.6824 (m-40) cc_final: 0.6325 (m110) REVERT: F 300 MET cc_start: 0.8337 (tpp) cc_final: 0.7937 (mmp) REVERT: F 319 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7601 (mp) REVERT: F 330 TYR cc_start: 0.5708 (t80) cc_final: 0.5387 (t80) REVERT: G 46 GLU cc_start: 0.8872 (tt0) cc_final: 0.8399 (tp30) REVERT: G 56 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7645 (mp0) REVERT: G 83 MET cc_start: 0.7133 (mtm) cc_final: 0.5816 (mpp) REVERT: H 27 PHE cc_start: 0.5867 (p90) cc_final: 0.5492 (p90) REVERT: H 68 PHE cc_start: 0.8062 (m-10) cc_final: 0.7343 (m-10) REVERT: I 32 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.4347 (m-70) REVERT: I 74 ASN cc_start: 0.6030 (m-40) cc_final: 0.5008 (p0) REVERT: J 36 TRP cc_start: 0.5710 (m100) cc_final: 0.4787 (m100) REVERT: J 51 ILE cc_start: 0.2345 (tt) cc_final: 0.1413 (mt) outliers start: 133 outliers final: 103 residues processed: 442 average time/residue: 0.4097 time to fit residues: 299.0701 Evaluate side-chains 431 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 310 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE 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 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 442 VAL Chi-restraints excluded: chain A residue 516 LYS 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 687 LEU 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 757 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL 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 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 396 GLU 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 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 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 159 ILE 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 303 THR 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 590 MET Chi-restraints excluded: chain C residue 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 757 THR 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 226 ARG 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 368 VAL Chi-restraints excluded: chain D residue 407 LEU 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 626 LEU Chi-restraints excluded: chain D residue 650 HIS 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 47 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 162 LEU 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 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU 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 G residue 69 THR 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 3 GLN 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 81 LEU 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 123 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 349 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 97 optimal weight: 0.2980 chunk 232 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 116 optimal weight: 0.0270 chunk 164 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN D 116 ASN ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080516 restraints weight = 79645.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.080919 restraints weight = 49204.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081323 restraints weight = 30517.627| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32012 Z= 0.141 Angle : 0.539 10.730 43388 Z= 0.278 Chirality : 0.041 0.193 4903 Planarity : 0.003 0.039 5371 Dihedral : 5.610 70.821 4239 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.92 % Allowed : 17.54 % Favored : 78.54 % 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: -0.17 (0.14), residues: 3759 helix: 0.50 (0.13), residues: 1673 sheet: -0.39 (0.22), residues: 616 loop : -0.54 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 36 HIS 0.006 0.001 HIS D 104 PHE 0.034 0.001 PHE D 611 TYR 0.043 0.001 TYR D 325 ARG 0.008 0.000 ARG J 72 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1482) hydrogen bonds : angle 4.16500 ( 3882) SS BOND : bond 0.00344 ( 20) SS BOND : angle 0.69679 ( 40) covalent geometry : bond 0.00323 (31992) covalent geometry : angle 0.53848 (43348) ********************** 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 450 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 314 time to evaluate : 3.431 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: 0.8974 (OUTLIER) cc_final: 0.8181 (t70) REVERT: A 154 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 161 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8222 (pp) REVERT: A 238 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 274 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (ttpp) REVERT: A 426 ASP cc_start: 0.7332 (t0) cc_final: 0.7119 (t0) REVERT: A 516 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6979 (tptp) REVERT: A 687 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (mt) REVERT: A 708 GLN cc_start: 0.7152 (mm110) cc_final: 0.6698 (mp10) REVERT: A 733 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 226 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6558 (mmm-85) REVERT: B 244 PHE cc_start: 0.6884 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: B 434 MET cc_start: 0.6975 (mmp) cc_final: 0.6349 (ttp) REVERT: B 444 ASP cc_start: 0.7843 (t70) cc_final: 0.7540 (t0) REVERT: B 448 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8705 (tp) REVERT: B 506 LYS cc_start: 0.8339 (pttm) cc_final: 0.7788 (tmtt) REVERT: B 590 MET cc_start: 0.8441 (mmm) cc_final: 0.7965 (mmm) REVERT: B 689 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7652 (m-80) REVERT: B 721 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6566 (pt0) REVERT: C 243 LEU cc_start: 0.9071 (tp) cc_final: 0.8845 (tp) REVERT: C 353 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6622 (t80) REVERT: C 377 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6913 (m170) REVERT: C 405 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7501 (mm) REVERT: C 422 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6783 (mmmm) REVERT: C 429 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: C 590 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.6020 (mmp) REVERT: C 688 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7566 (mtm-85) REVERT: D 135 ILE cc_start: 0.8865 (tt) cc_final: 0.8462 (mt) REVERT: D 218 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6968 (tmt170) REVERT: D 434 MET cc_start: 0.7848 (mmm) cc_final: 0.7345 (mmm) REVERT: D 446 VAL cc_start: 0.7942 (m) cc_final: 0.7261 (p) REVERT: D 454 GLU cc_start: 0.7397 (tt0) cc_final: 0.6996 (tp30) REVERT: D 459 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6714 (p) REVERT: D 467 GLN cc_start: 0.7076 (mt0) cc_final: 0.6737 (tm-30) REVERT: D 587 LEU cc_start: 0.8786 (mm) cc_final: 0.8537 (mm) REVERT: D 590 MET cc_start: 0.7563 (mpp) cc_final: 0.7287 (mpp) REVERT: D 592 ASN cc_start: 0.7960 (m-40) cc_final: 0.7394 (t0) REVERT: D 686 LYS cc_start: 0.7710 (mttp) cc_final: 0.7004 (mmmm) REVERT: E 46 GLN cc_start: 0.8501 (tp40) cc_final: 0.7817 (tm-30) REVERT: E 113 GLN cc_start: 0.7647 (mt0) cc_final: 0.7314 (mt0) REVERT: E 145 TRP cc_start: 0.5475 (t60) cc_final: 0.5080 (t60) REVERT: E 248 PHE cc_start: 0.6994 (t80) cc_final: 0.6442 (t80) REVERT: E 348 GLU cc_start: 0.5390 (mt-10) cc_final: 0.5075 (pm20) REVERT: F 44 THR cc_start: 0.8454 (m) cc_final: 0.8069 (p) REVERT: F 114 MET cc_start: 0.8956 (mmm) cc_final: 0.8497 (tpt) REVERT: F 156 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5119 (tm-30) REVERT: F 280 ASN cc_start: 0.6974 (m-40) cc_final: 0.6446 (m110) REVERT: F 300 MET cc_start: 0.8321 (tpp) cc_final: 0.7962 (mmp) REVERT: F 319 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7615 (mp) REVERT: F 330 TYR cc_start: 0.5753 (t80) cc_final: 0.5462 (t80) REVERT: G 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8383 (tp30) REVERT: G 56 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7631 (mp0) REVERT: G 83 MET cc_start: 0.7121 (mtm) cc_final: 0.5825 (mpp) REVERT: H 34 MET cc_start: 0.7299 (mmm) cc_final: 0.6853 (ttt) REVERT: H 68 PHE cc_start: 0.8010 (m-10) cc_final: 0.7282 (m-10) REVERT: I 32 HIS cc_start: 0.5846 (OUTLIER) cc_final: 0.4569 (m-70) REVERT: I 74 ASN cc_start: 0.6008 (m-40) cc_final: 0.4950 (p0) REVERT: J 36 TRP cc_start: 0.5694 (m100) cc_final: 0.4924 (m100) REVERT: J 51 ILE cc_start: 0.2327 (tt) cc_final: 0.2116 (mm) outliers start: 136 outliers final: 111 residues processed: 425 average time/residue: 0.4382 time to fit residues: 312.1337 Evaluate side-chains 432 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 301 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 97 ILE 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 274 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 314 LEU 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 516 LYS 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 687 LEU 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 733 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 60 VAL 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 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 396 GLU 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 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 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 159 ILE 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 303 THR 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 647 TRP Chi-restraints excluded: chain C residue 696 ASN Chi-restraints excluded: chain C residue 757 THR 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 161 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 226 ARG 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 368 VAL Chi-restraints excluded: chain D residue 407 LEU 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 626 LEU Chi-restraints excluded: chain D residue 650 HIS 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 47 VAL Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 162 LEU 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 31 LEU Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 103 LEU 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 G residue 69 THR 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 32 HIS Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 81 LEU 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 15 optimal weight: 0.9980 chunk 70 optimal weight: 0.0060 chunk 138 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 140 optimal weight: 0.5980 chunk 247 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 200 optimal weight: 0.3980 chunk 367 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS ** 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 = 0.3985 r_free = 0.3985 target = 0.118178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080926 restraints weight = 79031.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081214 restraints weight = 48594.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081661 restraints weight = 33511.359| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32012 Z= 0.110 Angle : 0.528 10.098 43388 Z= 0.271 Chirality : 0.040 0.258 4903 Planarity : 0.003 0.043 5371 Dihedral : 5.541 69.167 4239 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.57 % Allowed : 17.83 % Favored : 78.60 % 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: -0.12 (0.14), residues: 3759 helix: 0.54 (0.13), residues: 1680 sheet: -0.36 (0.22), residues: 614 loop : -0.52 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 36 HIS 0.005 0.001 HIS D 104 PHE 0.029 0.001 PHE D 611 TYR 0.041 0.001 TYR D 325 ARG 0.006 0.000 ARG G 31 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1482) hydrogen bonds : angle 4.08393 ( 3882) SS BOND : bond 0.00307 ( 20) SS BOND : angle 0.69729 ( 40) covalent geometry : bond 0.00247 (31992) covalent geometry : angle 0.52807 (43348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11019.01 seconds wall clock time: 192 minutes 9.86 seconds (11529.86 seconds total)