Starting phenix.real_space_refine on Mon Aug 25 22:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b41_15836/08_2025/8b41_15836.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b41_15836/08_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_15836/08_2025/8b41_15836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b41_15836/08_2025/8b41_15836.map" model { file = "/net/cci-nas-00/data/ceres_data/8b41_15836/08_2025/8b41_15836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b41_15836/08_2025/8b41_15836.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.42, per 1000 atoms: 0.24 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.18 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: 6.33 Time building geometry restraints manager: 3.32 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 28.420 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG F 18 TYR 0.013 0.001 TYR F 279 PHE 0.013 0.001 PHE C 250 TRP 0.010 0.001 TRP C 24 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00245 (31992) covalent geometry : angle 0.48189 (43348) SS BOND : bond 0.00355 ( 20) SS BOND : angle 0.80367 ( 40) hydrogen bonds : bond 0.16010 ( 1482) hydrogen bonds : angle 5.93134 ( 3882) *********************** 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 : 1.221 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: 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: 0.8339 (pp) REVERT: A 236 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7051 (pp20) REVERT: A 238 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8230 (mm-30) REVERT: A 410 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: A 426 ASP cc_start: 0.7072 (t0) cc_final: 0.6793 (t0) REVERT: A 546 LEU cc_start: 0.8267 (tp) cc_final: 0.7915 (tp) REVERT: A 583 VAL cc_start: 0.7422 (OUTLIER) cc_final: 0.7183 (t) REVERT: A 597 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7576 (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: 0.8531 (mp) REVERT: A 687 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8575 (mt) REVERT: A 769 LEU cc_start: 0.8413 (mt) cc_final: 0.8127 (tp) REVERT: B 226 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6696 (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: 0.7648 (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: 0.7925 (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: 0.7687 (mt) REVERT: C 243 LEU cc_start: 0.8945 (tp) cc_final: 0.8728 (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: 0.7929 (mp) REVERT: C 355 SER cc_start: 0.7332 (t) cc_final: 0.6798 (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: 0.5968 (pm20) REVERT: C 477 TYR cc_start: 0.8266 (m-10) cc_final: 0.8031 (m-10) REVERT: C 597 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7898 (mp0) REVERT: C 623 ASP cc_start: 0.8347 (t0) cc_final: 0.8101 (t0) REVERT: C 635 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: C 688 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7069 (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: 0.7642 (tp30) REVERT: D 135 ILE cc_start: 0.8834 (tt) cc_final: 0.8479 (mt) REVERT: D 173 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7941 (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: 0.8622 (p) REVERT: D 353 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7011 (t80) REVERT: D 422 LYS cc_start: 0.7378 (mtpt) cc_final: 0.7117 (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: 0.6655 (tm-30) REVERT: D 555 LEU cc_start: 0.7433 (mt) cc_final: 0.6883 (mp) REVERT: D 571 LYS cc_start: 0.8869 (tttm) cc_final: 0.8591 (ttpt) REVERT: D 587 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8145 (pp) REVERT: D 686 LYS cc_start: 0.7372 (mttp) cc_final: 0.6776 (mmmm) REVERT: E 46 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: E 99 LEU cc_start: 0.8904 (tp) cc_final: 0.8696 (tp) REVERT: E 117 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7737 (tm-30) REVERT: E 279 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7203 (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: 0.6545 (ttm) REVERT: E 379 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6847 (mm-40) REVERT: F 37 MET cc_start: 0.7937 (ttp) cc_final: 0.7667 (tpp) REVERT: F 44 THR cc_start: 0.8711 (m) cc_final: 0.8323 (p) REVERT: F 114 MET cc_start: 0.8564 (mmm) cc_final: 0.8223 (mmm) REVERT: F 156 GLU cc_start: 0.5142 (OUTLIER) cc_final: 0.4422 (tm-30) REVERT: F 297 ILE cc_start: 0.9298 (pt) cc_final: 0.9091 (pt) REVERT: F 334 CYS cc_start: 0.5454 (OUTLIER) cc_final: 0.4900 (t) REVERT: G 46 GLU cc_start: 0.8679 (tt0) cc_final: 0.8291 (tp30) REVERT: G 56 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7852 (mp0) REVERT: G 62 ASP cc_start: 0.7331 (m-30) cc_final: 0.7050 (p0) REVERT: G 104 TYR cc_start: 0.7988 (m-80) cc_final: 0.7443 (m-80) REVERT: H 13 GLN cc_start: 0.6879 (mp10) cc_final: 0.6483 (pm20) REVERT: H 86 LEU cc_start: 0.4799 (mt) cc_final: 0.3473 (mt) REVERT: H 87 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7610 (mmtm) REVERT: I 36 TRP cc_start: 0.5739 (m100) cc_final: 0.5388 (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: 0.5176 (m100) outliers start: 163 outliers final: 68 residues processed: 751 average time/residue: 0.2012 time to fit residues: 237.2644 Evaluate side-chains 443 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 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 740 ASN D 741 ASN E 46 GLN E 106 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 ASN H 110 GLN I 3 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080184 restraints weight = 79095.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.081972 restraints weight = 40967.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081858 restraints weight = 27563.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082556 restraints weight = 25115.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082490 restraints weight = 23126.245| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 32012 Z= 0.127 Angle : 0.558 10.025 43388 Z= 0.293 Chirality : 0.041 0.196 4903 Planarity : 0.004 0.037 5371 Dihedral : 7.167 70.005 4340 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.41 % Allowed : 12.53 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3759 helix: 0.37 (0.13), residues: 1665 sheet: -0.39 (0.21), residues: 640 loop : -0.54 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 545 TYR 0.022 0.001 TYR D 325 PHE 0.022 0.001 PHE B 250 TRP 0.014 0.001 TRP E 145 HIS 0.010 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00279 (31992) covalent geometry : angle 0.55716 (43348) SS BOND : bond 0.00327 ( 20) SS BOND : angle 0.84916 ( 40) hydrogen bonds : bond 0.04231 ( 1482) hydrogen bonds : angle 4.64398 ( 3882) *********************** 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 574 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 421 time to evaluate : 1.322 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: A 104 HIS cc_start: 0.9051 (OUTLIER) cc_final: 0.8368 (t70) REVERT: A 154 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: A 161 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8284 (pp) REVERT: A 238 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 410 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: A 426 ASP cc_start: 0.7050 (t0) cc_final: 0.6800 (t0) REVERT: A 546 LEU cc_start: 0.8287 (tp) cc_final: 0.8023 (tp) REVERT: A 626 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 687 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 733 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7548 (mp) REVERT: A 769 LEU cc_start: 0.8361 (mt) cc_final: 0.8131 (tp) REVERT: B 226 ARG cc_start: 0.6949 (mtp85) cc_final: 0.6746 (mmm-85) REVERT: B 238 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7425 (mt-10) REVERT: B 326 ILE cc_start: 0.8798 (pt) cc_final: 0.8567 (mt) REVERT: B 337 MET cc_start: 0.7413 (ppp) cc_final: 0.7195 (ppp) REVERT: B 410 GLU cc_start: 0.7630 (tp30) cc_final: 0.7284 (tp30) REVERT: B 444 ASP cc_start: 0.7952 (m-30) cc_final: 0.7742 (t0) REVERT: B 506 LYS cc_start: 0.8217 (pttm) cc_final: 0.7711 (tmtt) REVERT: B 674 ILE cc_start: 0.9287 (mm) cc_final: 0.9072 (mm) REVERT: B 689 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: B 721 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6429 (pt0) REVERT: B 806 ASP cc_start: 0.5698 (t70) cc_final: 0.5453 (t70) REVERT: C 52 MET cc_start: 0.8445 (mtp) cc_final: 0.8072 (mtp) REVERT: C 110 ASP cc_start: 0.8014 (m-30) cc_final: 0.7682 (t0) REVERT: C 348 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7943 (mp) REVERT: C 405 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7512 (mm) REVERT: C 422 LYS cc_start: 0.7145 (mtpt) cc_final: 0.6895 (mmmm) REVERT: C 429 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: C 448 LEU cc_start: 0.7239 (mp) cc_final: 0.6852 (mp) REVERT: C 482 LYS cc_start: 0.7842 (ptpp) cc_final: 0.7374 (mmmt) REVERT: C 584 LEU cc_start: 0.6862 (mt) cc_final: 0.6267 (tp) REVERT: C 590 MET cc_start: 0.5317 (mmp) cc_final: 0.5016 (mmp) REVERT: C 597 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7921 (mt-10) REVERT: C 688 ARG cc_start: 0.7600 (mtm110) cc_final: 0.7250 (mtm-85) REVERT: D 135 ILE cc_start: 0.8772 (tt) cc_final: 0.8408 (mt) REVERT: D 218 ARG cc_start: 0.7354 (ttt180) cc_final: 0.7069 (tmt170) REVERT: D 235 LYS cc_start: 0.7754 (mttt) cc_final: 0.7542 (ptpt) REVERT: D 353 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6952 (t80) REVERT: D 422 LYS cc_start: 0.7431 (mtpt) cc_final: 0.7230 (mmtt) REVERT: D 426 ASP cc_start: 0.8074 (t0) cc_final: 0.7779 (t0) REVERT: D 446 VAL cc_start: 0.7723 (m) cc_final: 0.6952 (p) REVERT: D 454 GLU cc_start: 0.7237 (tt0) cc_final: 0.6926 (tp30) REVERT: D 467 GLN cc_start: 0.6998 (mt0) cc_final: 0.6664 (tm-30) REVERT: D 545 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7673 (mtt180) REVERT: D 571 LYS cc_start: 0.8717 (tttm) cc_final: 0.8493 (ttpt) REVERT: D 590 MET cc_start: 0.6921 (mpp) cc_final: 0.6685 (mpp) REVERT: D 592 ASN cc_start: 0.7970 (m-40) cc_final: 0.7271 (t0) REVERT: D 635 PHE cc_start: 0.8408 (m-80) cc_final: 0.7933 (m-80) REVERT: D 686 LYS cc_start: 0.7450 (mttp) cc_final: 0.6913 (mmmm) REVERT: E 46 GLN cc_start: 0.8477 (tp40) cc_final: 0.7814 (tm-30) REVERT: E 99 LEU cc_start: 0.8916 (tp) cc_final: 0.8700 (tp) REVERT: E 112 ASN cc_start: 0.9002 (m-40) cc_final: 0.8667 (m-40) REVERT: E 117 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7706 (tm-30) REVERT: E 348 GLU cc_start: 0.6450 (mt-10) cc_final: 0.5530 (pm20) REVERT: E 373 MET cc_start: 0.6696 (mtp) cc_final: 0.6410 (ttm) REVERT: E 379 GLN cc_start: 0.7118 (mm110) cc_final: 0.6845 (mm-40) REVERT: F 37 MET cc_start: 0.7911 (ttp) cc_final: 0.7683 (tpp) REVERT: F 44 THR cc_start: 0.8643 (m) cc_final: 0.8239 (p) REVERT: F 330 TYR cc_start: 0.6239 (t80) cc_final: 0.5845 (t80) REVERT: G 46 GLU cc_start: 0.8782 (tt0) cc_final: 0.8354 (tp30) REVERT: G 56 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7781 (mp0) REVERT: G 104 TYR cc_start: 0.8043 (m-80) cc_final: 0.7459 (m-80) REVERT: H 13 GLN cc_start: 0.6846 (mp10) cc_final: 0.6602 (pp30) REVERT: I 3 GLN cc_start: 0.5570 (OUTLIER) cc_final: 0.4765 (pp30) REVERT: I 45 ARG cc_start: 0.5651 (ttm110) cc_final: 0.5403 (ttp-110) REVERT: I 46 GLU cc_start: 0.8200 (tt0) cc_final: 0.7671 (pm20) REVERT: I 74 ASN cc_start: 0.6229 (m-40) cc_final: 0.5398 (p0) REVERT: I 76 LYS cc_start: 0.7822 (mttm) cc_final: 0.7539 (mptt) REVERT: J 32 HIS cc_start: 0.6747 (m-70) cc_final: 0.6498 (m170) REVERT: J 36 TRP cc_start: 0.5869 (m100) cc_final: 0.4895 (m100) REVERT: J 105 TRP cc_start: 0.2586 (m-90) cc_final: 0.2242 (m-10) outliers start: 153 outliers final: 77 residues processed: 551 average time/residue: 0.2069 time to fit residues: 183.3098 Evaluate side-chains 435 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 344 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 257 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 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 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 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 295 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 354 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 J 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.117869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081618 restraints weight = 79477.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081523 restraints weight = 47650.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.081440 restraints weight = 32811.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.081913 restraints weight = 29029.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082034 restraints weight = 26383.066| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32012 Z= 0.145 Angle : 0.537 10.428 43388 Z= 0.283 Chirality : 0.041 0.160 4903 Planarity : 0.004 0.040 5371 Dihedral : 6.371 72.605 4277 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.84 % Allowed : 12.70 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3759 helix: 0.27 (0.13), residues: 1697 sheet: -0.38 (0.21), residues: 642 loop : -0.61 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 31 TYR 0.023 0.001 TYR C 477 PHE 0.023 0.001 PHE B 682 TRP 0.013 0.001 TRP I 36 HIS 0.008 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00324 (31992) covalent geometry : angle 0.53647 (43348) SS BOND : bond 0.00388 ( 20) SS BOND : angle 0.94953 ( 40) hydrogen bonds : bond 0.03929 ( 1482) hydrogen bonds : angle 4.49917 ( 3882) *********************** 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 544 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 376 time to evaluate : 1.324 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: A 104 HIS cc_start: 0.9000 (OUTLIER) cc_final: 0.8295 (t70) REVERT: A 154 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: A 161 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8258 (pp) REVERT: A 232 LEU cc_start: 0.4648 (OUTLIER) cc_final: 0.4427 (mp) REVERT: A 238 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 410 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7788 (tm-30) REVERT: A 426 ASP cc_start: 0.7015 (t0) cc_final: 0.6787 (t0) REVERT: A 516 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6843 (tptp) REVERT: A 546 LEU cc_start: 0.8280 (tp) cc_final: 0.8036 (tp) REVERT: A 593 LEU cc_start: 0.8628 (tp) cc_final: 0.8421 (tp) REVERT: A 687 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8566 (mt) REVERT: A 733 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7616 (mp) REVERT: B 226 ARG cc_start: 0.7010 (mtp85) cc_final: 0.6614 (mmm-85) REVERT: B 244 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5611 (m-80) REVERT: B 410 GLU cc_start: 0.7542 (tp30) cc_final: 0.7229 (tp30) REVERT: B 506 LYS cc_start: 0.8235 (pttm) cc_final: 0.7732 (tmtt) REVERT: B 689 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: B 791 PHE cc_start: 0.6749 (t80) cc_final: 0.6443 (t80) REVERT: C 238 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7958 (pt0) REVERT: C 348 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7809 (mp) REVERT: C 377 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7277 (m-70) REVERT: C 405 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7551 (mm) REVERT: C 422 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6919 (mmmm) REVERT: C 429 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: C 482 LYS cc_start: 0.7319 (ptpp) cc_final: 0.7031 (mmmt) REVERT: C 584 LEU cc_start: 0.6767 (mt) cc_final: 0.6294 (tp) REVERT: C 590 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.5101 (mmp) REVERT: C 635 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: C 688 ARG cc_start: 0.7499 (mtm110) cc_final: 0.7268 (mtm-85) REVERT: D 135 ILE cc_start: 0.8817 (tt) cc_final: 0.8428 (mt) REVERT: D 218 ARG cc_start: 0.7347 (ttt180) cc_final: 0.7053 (tmt170) REVERT: D 235 LYS cc_start: 0.7774 (mttt) cc_final: 0.7569 (ptpt) REVERT: D 434 MET cc_start: 0.7609 (mmm) cc_final: 0.7198 (mmm) REVERT: D 446 VAL cc_start: 0.7627 (m) cc_final: 0.6856 (p) REVERT: D 454 GLU cc_start: 0.7191 (tt0) cc_final: 0.6858 (tp30) REVERT: D 459 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6633 (p) REVERT: D 467 GLN cc_start: 0.7052 (mt0) cc_final: 0.6687 (tm-30) REVERT: D 545 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7662 (mtt180) REVERT: D 555 LEU cc_start: 0.6528 (mp) cc_final: 0.6116 (mp) REVERT: D 571 LYS cc_start: 0.8734 (tttm) cc_final: 0.8353 (ttpt) REVERT: D 590 MET cc_start: 0.7453 (mpp) cc_final: 0.7130 (mpp) REVERT: D 592 ASN cc_start: 0.7930 (m-40) cc_final: 0.7301 (t0) REVERT: D 635 PHE cc_start: 0.8455 (m-80) cc_final: 0.8001 (m-80) REVERT: D 647 TRP cc_start: 0.7180 (OUTLIER) cc_final: 0.6962 (p90) REVERT: D 686 LYS cc_start: 0.7490 (mttp) cc_final: 0.6951 (mmmm) REVERT: E 46 GLN cc_start: 0.8481 (tp40) cc_final: 0.7819 (tm-30) REVERT: E 48 MET cc_start: 0.7613 (ttt) cc_final: 0.7273 (ttm) REVERT: E 99 LEU cc_start: 0.8926 (tp) cc_final: 0.8557 (tt) REVERT: E 112 ASN cc_start: 0.9048 (m-40) cc_final: 0.8730 (m-40) REVERT: E 117 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7773 (tm-30) REVERT: E 261 MET cc_start: 0.4233 (ppp) cc_final: 0.3985 (ppp) REVERT: E 348 GLU cc_start: 0.5464 (mt-10) cc_final: 0.5239 (pm20) REVERT: E 373 MET cc_start: 0.6600 (mtp) cc_final: 0.6359 (ttm) REVERT: E 379 GLN cc_start: 0.7403 (mm110) cc_final: 0.7130 (mm-40) REVERT: F 44 THR cc_start: 0.8608 (m) cc_final: 0.8205 (p) REVERT: F 156 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4548 (tm-30) REVERT: F 280 ASN cc_start: 0.7322 (m-40) cc_final: 0.6982 (m110) REVERT: F 300 MET cc_start: 0.8275 (tpp) cc_final: 0.8002 (mmp) REVERT: F 330 TYR cc_start: 0.6034 (t80) cc_final: 0.5691 (t80) REVERT: G 46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8436 (tp30) REVERT: G 51 ILE cc_start: 0.8178 (tt) cc_final: 0.7889 (pt) REVERT: G 56 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7775 (mp0) REVERT: G 104 TYR cc_start: 0.8119 (m-80) cc_final: 0.7608 (m-80) REVERT: I 3 GLN cc_start: 0.5598 (OUTLIER) cc_final: 0.4833 (pp30) REVERT: I 27 PHE cc_start: 0.6631 (p90) cc_final: 0.5577 (p90) REVERT: I 37 TYR cc_start: 0.6231 (m-80) cc_final: 0.5959 (m-80) REVERT: I 74 ASN cc_start: 0.6034 (m-40) cc_final: 0.5010 (p0) REVERT: I 76 LYS cc_start: 0.7765 (mttm) cc_final: 0.7505 (mptt) REVERT: J 36 TRP cc_start: 0.5722 (m100) cc_final: 0.4879 (m100) REVERT: J 51 ILE cc_start: 0.2658 (tp) cc_final: 0.1560 (mm) REVERT: J 105 TRP cc_start: 0.2652 (m-90) cc_final: 0.2304 (m-10) outliers start: 168 outliers final: 99 residues processed: 512 average time/residue: 0.2054 time to fit residues: 170.5519 Evaluate side-chains 451 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 332 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 353 PHE Chi-restraints excluded: chain A residue 410 GLU 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 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 20 LEU 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 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 337 MET Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 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 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 36 LEU 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 E residue 20 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 3 GLN Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 93 VAL 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 354 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 140 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 478 HIS ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 614 HIS D 431 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 HIS ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.117752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081520 restraints weight = 78797.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081513 restraints weight = 45590.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081542 restraints weight = 31131.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081904 restraints weight = 28384.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082047 restraints weight = 25918.369| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32012 Z= 0.134 Angle : 0.522 8.964 43388 Z= 0.274 Chirality : 0.040 0.151 4903 Planarity : 0.003 0.038 5371 Dihedral : 6.095 71.561 4259 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.61 % Allowed : 14.17 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.14), residues: 3759 helix: 0.27 (0.13), residues: 1707 sheet: -0.51 (0.22), residues: 602 loop : -0.60 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 31 TYR 0.029 0.001 TYR C 477 PHE 0.024 0.001 PHE F 41 TRP 0.025 0.001 TRP I 36 HIS 0.007 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00304 (31992) covalent geometry : angle 0.52138 (43348) SS BOND : bond 0.00357 ( 20) SS BOND : angle 0.84563 ( 40) hydrogen bonds : bond 0.03687 ( 1482) hydrogen bonds : angle 4.36944 ( 3882) *********************** 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: 160 poor density : 351 time to evaluate : 1.273 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: A 104 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8357 (t70) REVERT: A 154 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: A 161 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8240 (pp) REVERT: A 238 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 415 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7850 (ttpm) REVERT: A 426 ASP cc_start: 0.7188 (t0) cc_final: 0.6959 (t0) REVERT: A 516 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6915 (tptp) REVERT: A 546 LEU cc_start: 0.8311 (tp) cc_final: 0.8071 (tp) REVERT: A 593 LEU cc_start: 0.8662 (tp) cc_final: 0.8435 (tp) REVERT: A 626 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 687 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 733 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7555 (mp) REVERT: B 115 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7576 (tp30) REVERT: B 226 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6584 (mmm-85) REVERT: B 244 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: B 350 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5317 (ttpp) REVERT: B 410 GLU cc_start: 0.7511 (tp30) cc_final: 0.7214 (tp30) REVERT: B 448 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8706 (tp) REVERT: B 506 LYS cc_start: 0.8193 (pttm) cc_final: 0.7733 (tmtt) REVERT: B 689 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: B 721 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6426 (pt0) REVERT: B 791 PHE cc_start: 0.6789 (t80) cc_final: 0.6496 (t80) REVERT: C 110 ASP cc_start: 0.8157 (m-30) cc_final: 0.7833 (t0) REVERT: C 377 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7320 (m-70) REVERT: C 405 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7447 (mm) REVERT: C 422 LYS cc_start: 0.7262 (mtpt) cc_final: 0.6861 (mmmm) REVERT: C 429 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6491 (pm20) REVERT: C 482 LYS cc_start: 0.7547 (ptpp) cc_final: 0.7211 (tttt) REVERT: C 590 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5464 (mmp) REVERT: C 635 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6949 (m-10) REVERT: C 688 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7141 (mtm-85) REVERT: D 135 ILE cc_start: 0.8817 (tt) cc_final: 0.8429 (mt) REVERT: D 218 ARG cc_start: 0.7259 (ttt180) cc_final: 0.7009 (tmt170) REVERT: D 235 LYS cc_start: 0.7785 (mttt) cc_final: 0.7570 (ptpt) REVERT: D 434 MET cc_start: 0.7724 (mmm) cc_final: 0.7272 (mmm) REVERT: D 446 VAL cc_start: 0.7690 (m) cc_final: 0.6916 (p) REVERT: D 454 GLU cc_start: 0.7204 (tt0) cc_final: 0.6846 (tp30) REVERT: D 459 VAL cc_start: 0.6930 (OUTLIER) cc_final: 0.6626 (p) REVERT: D 467 GLN cc_start: 0.7054 (mt0) cc_final: 0.6677 (tm-30) REVERT: D 555 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6539 (mt) REVERT: D 571 LYS cc_start: 0.8705 (tttm) cc_final: 0.8493 (ttpt) REVERT: D 592 ASN cc_start: 0.7937 (m-40) cc_final: 0.7271 (t0) REVERT: D 647 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6910 (p90) REVERT: D 686 LYS cc_start: 0.7504 (mttp) cc_final: 0.6889 (mmmm) REVERT: E 46 GLN cc_start: 0.8473 (tp40) cc_final: 0.7786 (tm-30) REVERT: E 99 LEU cc_start: 0.8922 (tp) cc_final: 0.8532 (tt) REVERT: E 112 ASN cc_start: 0.9040 (m-40) cc_final: 0.8787 (m-40) REVERT: E 117 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7849 (tm-30) REVERT: E 348 GLU cc_start: 0.5338 (mt-10) cc_final: 0.5097 (pm20) REVERT: E 373 MET cc_start: 0.6503 (mtp) cc_final: 0.6252 (ttm) REVERT: E 379 GLN cc_start: 0.7414 (mm110) cc_final: 0.7134 (mm-40) REVERT: F 44 THR cc_start: 0.8503 (m) cc_final: 0.8124 (p) REVERT: F 117 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7358 (tm-30) REVERT: F 156 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.4918 (tm-30) REVERT: F 276 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6110 (mm) REVERT: F 280 ASN cc_start: 0.7264 (m-40) cc_final: 0.6887 (m110) REVERT: G 34 MET cc_start: 0.7885 (mmt) cc_final: 0.7419 (mmt) REVERT: G 46 GLU cc_start: 0.8857 (tt0) cc_final: 0.8440 (tp30) REVERT: G 56 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7803 (mp0) REVERT: I 3 GLN cc_start: 0.5290 (pp30) cc_final: 0.4530 (pp30) REVERT: I 74 ASN cc_start: 0.6033 (m-40) cc_final: 0.5046 (p0) REVERT: J 31 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7779 (ptt-90) REVERT: J 36 TRP cc_start: 0.5613 (m100) cc_final: 0.4785 (m100) REVERT: J 51 ILE cc_start: 0.2578 (tp) cc_final: 0.1539 (mm) REVERT: J 105 TRP cc_start: 0.2579 (m-90) cc_final: 0.2240 (m-10) outliers start: 160 outliers final: 101 residues processed: 478 average time/residue: 0.2069 time to fit residues: 160.4356 Evaluate side-chains 439 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 315 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 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 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 161 LEU Chi-restraints excluded: chain B residue 163 CYS 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 459 VAL Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 647 TRP Chi-restraints excluded: chain B residue 689 TYR Chi-restraints excluded: chain B residue 721 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain C residue 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 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 635 PHE 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 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 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 156 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 344 optimal weight: 8.9990 chunk 154 optimal weight: 0.5980 chunk 299 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 132 HIS ** 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 ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** 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 = 0.3975 r_free = 0.3975 target = 0.117556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080428 restraints weight = 79581.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080792 restraints weight = 48047.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.080834 restraints weight = 32318.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081138 restraints weight = 31505.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081396 restraints weight = 26702.299| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32012 Z= 0.114 Angle : 0.514 9.161 43388 Z= 0.268 Chirality : 0.040 0.158 4903 Planarity : 0.003 0.043 5371 Dihedral : 5.806 70.665 4256 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.21 % Allowed : 15.41 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3759 helix: 0.39 (0.13), residues: 1691 sheet: -0.35 (0.22), residues: 613 loop : -0.61 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 31 TYR 0.023 0.001 TYR D 325 PHE 0.014 0.001 PHE C 353 TRP 0.011 0.001 TRP I 36 HIS 0.013 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00256 (31992) covalent geometry : angle 0.51406 (43348) SS BOND : bond 0.00345 ( 20) SS BOND : angle 0.76863 ( 40) hydrogen bonds : bond 0.03504 ( 1482) hydrogen bonds : angle 4.24846 ( 3882) *********************** 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 489 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 343 time to evaluate : 1.369 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: 0.8998 (OUTLIER) cc_final: 0.8216 (t70) REVERT: A 154 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: A 161 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 238 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 415 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7891 (ttpm) REVERT: A 426 ASP cc_start: 0.7265 (t0) cc_final: 0.7038 (t0) REVERT: A 516 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6792 (tptp) REVERT: A 546 LEU cc_start: 0.8317 (tp) cc_final: 0.8065 (tp) REVERT: A 626 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 687 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 733 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 226 ARG cc_start: 0.6983 (mtp85) cc_final: 0.6540 (mmm-85) REVERT: B 244 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: B 410 GLU cc_start: 0.7469 (tp30) cc_final: 0.7218 (tp30) REVERT: B 434 MET cc_start: 0.6622 (mmp) cc_final: 0.6129 (mtp) REVERT: B 444 ASP cc_start: 0.7523 (t70) cc_final: 0.7237 (t0) REVERT: B 448 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 506 LYS cc_start: 0.8384 (pttm) cc_final: 0.7773 (tmtt) REVERT: B 689 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 721 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: B 791 PHE cc_start: 0.6745 (t80) cc_final: 0.6517 (t80) REVERT: C 377 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7294 (m-70) REVERT: C 405 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 422 LYS cc_start: 0.7227 (mtpt) cc_final: 0.6808 (mmmm) REVERT: C 429 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6458 (pm20) REVERT: C 590 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5462 (mmp) REVERT: C 597 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7803 (mp0) REVERT: C 688 ARG cc_start: 0.7541 (mtm110) cc_final: 0.7221 (mtm-85) REVERT: D 135 ILE cc_start: 0.8818 (tt) cc_final: 0.8433 (mt) REVERT: D 218 ARG cc_start: 0.7243 (ttt180) cc_final: 0.6958 (tmt170) REVERT: D 235 LYS cc_start: 0.7782 (mttt) cc_final: 0.7565 (ptpt) REVERT: D 434 MET cc_start: 0.7759 (mmm) cc_final: 0.7312 (mmm) REVERT: D 446 VAL cc_start: 0.7742 (m) cc_final: 0.6961 (p) REVERT: D 454 GLU cc_start: 0.7241 (tt0) cc_final: 0.6832 (tp30) REVERT: D 459 VAL cc_start: 0.6632 (OUTLIER) cc_final: 0.6322 (p) REVERT: D 467 GLN cc_start: 0.7045 (mt0) cc_final: 0.6667 (tm-30) REVERT: D 555 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6511 (mt) REVERT: D 592 ASN cc_start: 0.7968 (m-40) cc_final: 0.7385 (t0) REVERT: D 647 TRP cc_start: 0.7117 (OUTLIER) cc_final: 0.6895 (p90) REVERT: D 686 LYS cc_start: 0.7498 (mttp) cc_final: 0.6827 (mmmm) REVERT: E 46 GLN cc_start: 0.8503 (tp40) cc_final: 0.7835 (tm-30) REVERT: E 112 ASN cc_start: 0.8940 (m-40) cc_final: 0.8696 (m-40) REVERT: E 113 GLN cc_start: 0.7540 (mt0) cc_final: 0.6748 (mt0) REVERT: E 117 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7894 (tm-30) REVERT: E 248 PHE cc_start: 0.6918 (t80) cc_final: 0.6649 (t80) REVERT: E 348 GLU cc_start: 0.5388 (mt-10) cc_final: 0.5101 (pm20) REVERT: F 44 THR cc_start: 0.8461 (m) cc_final: 0.8067 (p) REVERT: F 156 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5143 (tm-30) REVERT: F 276 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.6009 (mm) REVERT: F 280 ASN cc_start: 0.6829 (m-40) cc_final: 0.6401 (m110) REVERT: F 300 MET cc_start: 0.8307 (tpp) cc_final: 0.7957 (mmp) REVERT: F 330 TYR cc_start: 0.5980 (t80) cc_final: 0.5658 (t80) REVERT: G 34 MET cc_start: 0.7885 (mmt) cc_final: 0.7359 (mmt) REVERT: G 46 GLU cc_start: 0.8898 (tt0) cc_final: 0.8458 (tp30) REVERT: G 51 ILE cc_start: 0.8129 (tt) cc_final: 0.7911 (pt) REVERT: G 56 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7800 (mp0) REVERT: I 3 GLN cc_start: 0.5363 (OUTLIER) cc_final: 0.4584 (pp30) REVERT: I 74 ASN cc_start: 0.6035 (m-40) cc_final: 0.4981 (p0) REVERT: J 31 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7722 (ptt-90) REVERT: J 36 TRP cc_start: 0.5829 (m100) cc_final: 0.4826 (m100) REVERT: J 105 TRP cc_start: 0.2262 (m-90) cc_final: 0.1962 (m-10) outliers start: 146 outliers final: 100 residues processed: 463 average time/residue: 0.2103 time to fit residues: 158.8783 Evaluate side-chains 435 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 313 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 727 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 750 VAL 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 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 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 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 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 170 THR Chi-restraints excluded: chain C residue 231 VAL 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 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 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 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 626 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 20 LEU Chi-restraints excluded: chain E residue 32 SER 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 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 156 GLU 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 F residue 322 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 119 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 208 optimal weight: 0.0670 chunk 212 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.117348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080431 restraints weight = 79301.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080643 restraints weight = 50627.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080754 restraints weight = 32957.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081318 restraints weight = 29096.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081377 restraints weight = 26062.436| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32012 Z= 0.138 Angle : 0.525 8.295 43388 Z= 0.273 Chirality : 0.040 0.150 4903 Planarity : 0.003 0.039 5371 Dihedral : 5.704 71.363 4248 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.44 % Allowed : 15.61 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3759 helix: 0.38 (0.13), residues: 1690 sheet: -0.38 (0.22), residues: 615 loop : -0.61 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 31 TYR 0.031 0.001 TYR D 325 PHE 0.026 0.001 PHE F 41 TRP 0.011 0.001 TRP F 340 HIS 0.010 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00315 (31992) covalent geometry : angle 0.52425 (43348) SS BOND : bond 0.00396 ( 20) SS BOND : angle 0.81083 ( 40) hydrogen bonds : bond 0.03512 ( 1482) hydrogen bonds : angle 4.23765 ( 3882) *********************** 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 491 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 337 time to evaluate : 1.208 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: A 104 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8233 (t70) REVERT: A 154 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: A 161 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (pp) REVERT: A 238 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8022 (mm-30) REVERT: A 415 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7879 (ttpm) REVERT: A 426 ASP cc_start: 0.7269 (t0) cc_final: 0.7044 (t0) REVERT: A 516 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6755 (tptp) REVERT: A 546 LEU cc_start: 0.8308 (tp) cc_final: 0.8079 (tp) REVERT: A 626 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 687 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 733 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7574 (mp) REVERT: B 115 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7737 (tp30) REVERT: B 226 ARG cc_start: 0.6993 (mtp85) cc_final: 0.6563 (mmm-85) REVERT: B 244 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5561 (m-80) REVERT: B 350 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5414 (ttpp) REVERT: B 410 GLU cc_start: 0.7425 (tp30) cc_final: 0.7203 (tp30) REVERT: B 434 MET cc_start: 0.6538 (mmp) cc_final: 0.6019 (mtp) REVERT: B 444 ASP cc_start: 0.7839 (t70) cc_final: 0.7505 (t0) REVERT: B 448 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 506 LYS cc_start: 0.8359 (pttm) cc_final: 0.7774 (tmtt) REVERT: B 590 MET cc_start: 0.8428 (mmm) cc_final: 0.8012 (mmm) REVERT: B 689 TYR cc_start: 0.7986 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: B 721 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6396 (pt0) REVERT: B 791 PHE cc_start: 0.6753 (t80) cc_final: 0.6507 (t80) REVERT: C 353 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6631 (t80) REVERT: C 377 HIS cc_start: 0.7564 (OUTLIER) cc_final: 0.6951 (m170) REVERT: C 405 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 422 LYS cc_start: 0.7281 (mtpt) cc_final: 0.6866 (mmmm) REVERT: C 429 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6484 (pm20) REVERT: C 590 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5672 (mmp) REVERT: C 597 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 635 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: D 135 ILE cc_start: 0.8839 (tt) cc_final: 0.8443 (mt) REVERT: D 218 ARG cc_start: 0.7267 (ttt180) cc_final: 0.6994 (tmt170) REVERT: D 235 LYS cc_start: 0.7794 (mttt) cc_final: 0.7583 (ptpt) REVERT: D 434 MET cc_start: 0.7759 (mmm) cc_final: 0.7305 (mmm) REVERT: D 446 VAL cc_start: 0.7657 (m) cc_final: 0.6872 (p) REVERT: D 454 GLU cc_start: 0.7225 (tt0) cc_final: 0.6837 (tp30) REVERT: D 459 VAL cc_start: 0.7016 (OUTLIER) cc_final: 0.6718 (p) REVERT: D 467 GLN cc_start: 0.7060 (mt0) cc_final: 0.6678 (tm-30) REVERT: D 555 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6479 (mt) REVERT: D 587 LEU cc_start: 0.8357 (mm) cc_final: 0.7940 (mm) REVERT: D 590 MET cc_start: 0.6859 (mpp) cc_final: 0.6111 (mpp) REVERT: D 592 ASN cc_start: 0.7890 (m-40) cc_final: 0.7336 (t0) REVERT: D 647 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6964 (p90) REVERT: D 686 LYS cc_start: 0.7811 (mttp) cc_final: 0.7097 (mmmm) REVERT: E 46 GLN cc_start: 0.8506 (tp40) cc_final: 0.7806 (tm-30) REVERT: E 112 ASN cc_start: 0.9036 (m-40) cc_final: 0.8807 (m110) REVERT: E 117 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7869 (tm-30) REVERT: E 157 HIS cc_start: 0.5570 (m170) cc_final: 0.5239 (m170) REVERT: E 248 PHE cc_start: 0.6816 (t80) cc_final: 0.6473 (t80) REVERT: E 348 GLU cc_start: 0.5356 (mt-10) cc_final: 0.5078 (pm20) REVERT: F 44 THR cc_start: 0.8487 (m) cc_final: 0.8080 (p) REVERT: F 156 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.4988 (tm-30) REVERT: F 276 ILE cc_start: 0.6421 (OUTLIER) cc_final: 0.6165 (mm) REVERT: F 280 ASN cc_start: 0.6987 (m-40) cc_final: 0.6553 (m110) REVERT: F 300 MET cc_start: 0.8304 (tpp) cc_final: 0.7955 (mmp) REVERT: F 330 TYR cc_start: 0.6109 (t80) cc_final: 0.5826 (t80) REVERT: G 34 MET cc_start: 0.7856 (mmt) cc_final: 0.7360 (mmt) REVERT: G 46 GLU cc_start: 0.8880 (tt0) cc_final: 0.8438 (tp30) REVERT: G 51 ILE cc_start: 0.8088 (tt) cc_final: 0.7858 (pt) REVERT: G 56 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7786 (mp0) REVERT: I 32 HIS cc_start: 0.5346 (OUTLIER) cc_final: 0.3975 (m-70) REVERT: I 74 ASN cc_start: 0.6016 (m-40) cc_final: 0.4943 (p0) REVERT: J 31 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7702 (ptt-90) REVERT: J 36 TRP cc_start: 0.5757 (m100) cc_final: 0.4836 (m100) outliers start: 154 outliers final: 109 residues processed: 461 average time/residue: 0.1968 time to fit residues: 148.6980 Evaluate side-chains 446 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 312 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 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 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 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 A residue 750 VAL Chi-restraints excluded: chain A residue 757 THR 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 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 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 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 303 THR Chi-restraints excluded: chain C residue 339 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 450 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 568 HIS Chi-restraints excluded: chain C residue 590 MET Chi-restraints excluded: chain C residue 635 PHE Chi-restraints excluded: chain C residue 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 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 555 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 647 TRP Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 118 ARG 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 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 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 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 48 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 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 114 optimal weight: 0.7980 chunk 242 optimal weight: 0.0980 chunk 270 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 D 576 ASN D 712 ASN D 755 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.117997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081163 restraints weight = 79569.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081750 restraints weight = 46155.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081492 restraints weight = 33358.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081886 restraints weight = 32827.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082060 restraints weight = 27755.531| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 32012 Z= 0.109 Angle : 0.506 9.844 43388 Z= 0.264 Chirality : 0.040 0.233 4903 Planarity : 0.003 0.036 5371 Dihedral : 5.578 69.794 4245 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.29 % Allowed : 15.96 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.14), residues: 3759 helix: 0.46 (0.13), residues: 1689 sheet: -0.35 (0.22), residues: 615 loop : -0.58 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 31 TYR 0.035 0.001 TYR D 325 PHE 0.025 0.001 PHE F 41 TRP 0.012 0.001 TRP F 340 HIS 0.008 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00244 (31992) covalent geometry : angle 0.50604 (43348) SS BOND : bond 0.00334 ( 20) SS BOND : angle 0.82495 ( 40) hydrogen bonds : bond 0.03363 ( 1482) hydrogen bonds : angle 4.13385 ( 3882) *********************** 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 495 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 346 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8157 (t70) REVERT: A 154 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: A 161 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8263 (pp) REVERT: A 238 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8020 (mm-30) REVERT: A 415 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7884 (ttpm) REVERT: A 426 ASP cc_start: 0.7285 (t0) cc_final: 0.7063 (t0) REVERT: A 516 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6879 (tptp) REVERT: A 540 LEU cc_start: 0.8988 (tp) cc_final: 0.8747 (tp) REVERT: A 593 LEU cc_start: 0.8787 (tp) cc_final: 0.8506 (tp) REVERT: A 687 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 733 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 115 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7627 (tp30) REVERT: B 226 ARG cc_start: 0.6963 (mtp85) cc_final: 0.6529 (mmm-85) REVERT: B 244 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: B 410 GLU cc_start: 0.7401 (tp30) cc_final: 0.7188 (tp30) REVERT: B 434 MET cc_start: 0.6486 (mmp) cc_final: 0.6038 (mtp) REVERT: B 444 ASP cc_start: 0.7768 (t70) cc_final: 0.7438 (t0) REVERT: B 448 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 506 LYS cc_start: 0.8366 (pttm) cc_final: 0.7778 (tmtt) REVERT: B 590 MET cc_start: 0.8418 (mmm) cc_final: 0.7981 (mmm) REVERT: B 674 ILE cc_start: 0.9283 (mm) cc_final: 0.9075 (mm) REVERT: B 689 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: B 721 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6385 (pt0) REVERT: B 791 PHE cc_start: 0.6830 (t80) cc_final: 0.6524 (t80) REVERT: C 353 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6593 (t80) REVERT: C 377 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6933 (m170) REVERT: C 405 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 422 LYS cc_start: 0.7245 (mtpt) cc_final: 0.6844 (mmmm) REVERT: C 590 MET cc_start: 0.5952 (OUTLIER) cc_final: 0.5687 (mmp) REVERT: D 135 ILE cc_start: 0.8808 (tt) cc_final: 0.8394 (mt) REVERT: D 218 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6950 (tmt170) REVERT: D 235 LYS cc_start: 0.7797 (mttt) cc_final: 0.7576 (ptpt) REVERT: D 434 MET cc_start: 0.7839 (mmm) cc_final: 0.7344 (mmm) REVERT: D 446 VAL cc_start: 0.7881 (m) cc_final: 0.7148 (p) REVERT: D 454 GLU cc_start: 0.7355 (tt0) cc_final: 0.6941 (tp30) REVERT: D 459 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6442 (p) REVERT: D 467 GLN cc_start: 0.7045 (mt0) cc_final: 0.6678 (tm-30) REVERT: D 555 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6652 (mt) REVERT: D 571 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8372 (ttmm) REVERT: D 592 ASN cc_start: 0.7890 (m-40) cc_final: 0.7336 (t0) REVERT: D 686 LYS cc_start: 0.7707 (mttp) cc_final: 0.6995 (mmmm) REVERT: E 46 GLN cc_start: 0.8483 (tp40) cc_final: 0.7849 (tm-30) REVERT: E 112 ASN cc_start: 0.8885 (m-40) cc_final: 0.8640 (m-40) REVERT: E 113 GLN cc_start: 0.7310 (mt0) cc_final: 0.7105 (mt0) REVERT: E 117 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 248 PHE cc_start: 0.6824 (t80) cc_final: 0.6466 (t80) REVERT: E 348 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4970 (pm20) REVERT: F 44 THR cc_start: 0.8434 (m) cc_final: 0.8027 (p) REVERT: F 156 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: F 276 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5819 (mm) REVERT: F 280 ASN cc_start: 0.6897 (m-40) cc_final: 0.6440 (m110) REVERT: F 300 MET cc_start: 0.8294 (tpp) cc_final: 0.7956 (mmp) REVERT: F 330 TYR cc_start: 0.5723 (t80) cc_final: 0.5433 (t80) REVERT: G 34 MET cc_start: 0.7831 (mmt) cc_final: 0.7283 (mmt) REVERT: G 46 GLU cc_start: 0.8870 (tt0) cc_final: 0.8410 (tp30) REVERT: G 51 ILE cc_start: 0.8117 (tt) cc_final: 0.7900 (pt) REVERT: G 56 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7808 (mp0) REVERT: H 34 MET cc_start: 0.7361 (mmt) cc_final: 0.6687 (mmp) REVERT: H 46 GLU cc_start: 0.7991 (tp30) cc_final: 0.7573 (pp20) REVERT: I 74 ASN cc_start: 0.6017 (m-40) cc_final: 0.4953 (p0) REVERT: J 36 TRP cc_start: 0.5866 (m100) cc_final: 0.4930 (m100) outliers start: 149 outliers final: 106 residues processed: 464 average time/residue: 0.1964 time to fit residues: 150.2080 Evaluate side-chains 443 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 318 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 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 344 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 415 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 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 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 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 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 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 40 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 339 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 450 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 565 VAL Chi-restraints excluded: chain C residue 590 MET 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 161 LEU 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 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 555 LEU Chi-restraints excluded: chain D residue 561 VAL 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 20 LEU 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 162 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 339 TYR Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 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 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 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 67 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 127 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 chunk 354 optimal weight: 0.0970 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 295 optimal weight: 0.0980 chunk 174 optimal weight: 0.6980 chunk 188 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 239 GLN E 106 GLN E 113 GLN F 113 GLN ** J 32 HIS ** 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 = 0.3991 r_free = 0.3991 target = 0.118433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081223 restraints weight = 79103.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082041 restraints weight = 46041.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.082314 restraints weight = 30133.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.082676 restraints weight = 27070.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082806 restraints weight = 24301.007| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 32012 Z= 0.102 Angle : 0.508 9.779 43388 Z= 0.263 Chirality : 0.040 0.202 4903 Planarity : 0.003 0.039 5371 Dihedral : 5.425 68.978 4238 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.83 % Allowed : 16.76 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3759 helix: 0.55 (0.13), residues: 1682 sheet: -0.33 (0.22), residues: 615 loop : -0.50 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 118 TYR 0.036 0.001 TYR D 325 PHE 0.025 0.001 PHE F 41 TRP 0.021 0.001 TRP D 647 HIS 0.007 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00225 (31992) covalent geometry : angle 0.50768 (43348) SS BOND : bond 0.00294 ( 20) SS BOND : angle 0.77093 ( 40) hydrogen bonds : bond 0.03272 ( 1482) hydrogen bonds : angle 4.05190 ( 3882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7518 Ramachandran restraints generated. 3759 Oldfield, 0 Emsley, 3759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 343 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8199 (t70) REVERT: A 154 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: A 157 VAL cc_start: 0.9040 (t) cc_final: 0.8725 (p) REVERT: A 238 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 426 ASP cc_start: 0.7290 (t0) cc_final: 0.7078 (t0) REVERT: A 516 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6860 (tptp) REVERT: A 540 LEU cc_start: 0.8957 (tp) cc_final: 0.8708 (tp) REVERT: A 593 LEU cc_start: 0.8600 (tp) cc_final: 0.8366 (tp) REVERT: A 687 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8438 (mt) REVERT: A 733 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7695 (mp) REVERT: B 115 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7695 (tp30) REVERT: B 226 ARG cc_start: 0.6955 (mtp85) cc_final: 0.6514 (mmm-85) REVERT: B 244 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: B 434 MET cc_start: 0.6409 (mmp) cc_final: 0.5998 (mtp) REVERT: B 444 ASP cc_start: 0.7796 (t70) cc_final: 0.7497 (t0) REVERT: B 506 LYS cc_start: 0.8357 (pttm) cc_final: 0.7772 (tmtt) REVERT: B 590 MET cc_start: 0.8412 (mmm) cc_final: 0.7938 (mmm) REVERT: B 689 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: B 721 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6476 (pt0) REVERT: B 791 PHE cc_start: 0.6824 (t80) cc_final: 0.6431 (t80) REVERT: C 281 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8771 (p90) REVERT: C 353 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6590 (t80) REVERT: C 377 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6903 (m170) REVERT: C 405 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7488 (mm) REVERT: C 422 LYS cc_start: 0.7259 (mtpt) cc_final: 0.6789 (mmmm) REVERT: C 429 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: C 471 LEU cc_start: 0.7947 (tp) cc_final: 0.7730 (tp) REVERT: C 590 MET cc_start: 0.5888 (mmp) cc_final: 0.5641 (mmp) REVERT: C 597 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7883 (mp0) REVERT: D 104 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7913 (t70) REVERT: D 135 ILE cc_start: 0.8802 (tt) cc_final: 0.8389 (mt) REVERT: D 218 ARG cc_start: 0.7254 (ttt180) cc_final: 0.6959 (tmt170) REVERT: D 235 LYS cc_start: 0.7801 (mttt) cc_final: 0.7586 (ptpt) REVERT: D 434 MET cc_start: 0.7846 (mmm) cc_final: 0.7336 (mmm) REVERT: D 446 VAL cc_start: 0.7893 (m) cc_final: 0.7184 (p) REVERT: D 454 GLU cc_start: 0.7343 (tt0) cc_final: 0.6912 (tp30) REVERT: D 459 VAL cc_start: 0.6722 (OUTLIER) cc_final: 0.6413 (p) REVERT: D 467 GLN cc_start: 0.6995 (mt0) cc_final: 0.6675 (tm-30) REVERT: D 555 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6573 (mt) REVERT: D 571 LYS cc_start: 0.8727 (ttpt) cc_final: 0.8400 (ttmm) REVERT: D 592 ASN cc_start: 0.7887 (m-40) cc_final: 0.7349 (t0) REVERT: D 686 LYS cc_start: 0.7655 (mttp) cc_final: 0.6985 (mmmm) REVERT: E 46 GLN cc_start: 0.8535 (tp40) cc_final: 0.7919 (tm-30) REVERT: E 112 ASN cc_start: 0.8809 (m-40) cc_final: 0.8590 (m-40) REVERT: E 248 PHE cc_start: 0.7005 (t80) cc_final: 0.6548 (t80) REVERT: E 348 GLU cc_start: 0.5290 (mt-10) cc_final: 0.5031 (pm20) REVERT: F 44 THR cc_start: 0.8388 (m) cc_final: 0.8005 (p) REVERT: F 156 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5657 (tm-30) REVERT: F 280 ASN cc_start: 0.6832 (m-40) cc_final: 0.6386 (m110) REVERT: F 300 MET cc_start: 0.8299 (tpp) cc_final: 0.7921 (mmp) REVERT: F 330 TYR cc_start: 0.5682 (t80) cc_final: 0.5367 (t80) REVERT: G 34 MET cc_start: 0.7978 (mmt) cc_final: 0.7469 (mmt) REVERT: G 46 GLU cc_start: 0.8850 (tt0) cc_final: 0.8428 (tp30) REVERT: G 51 ILE cc_start: 0.8103 (tt) cc_final: 0.7896 (pt) REVERT: G 56 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7746 (mp0) REVERT: G 107 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6174 (pm20) REVERT: H 34 MET cc_start: 0.7344 (mmt) cc_final: 0.6628 (ttm) REVERT: H 46 GLU cc_start: 0.7921 (tp30) cc_final: 0.7522 (pp20) REVERT: I 32 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.3609 (m-70) REVERT: I 74 ASN cc_start: 0.5959 (m-40) cc_final: 0.4905 (p0) REVERT: J 36 TRP cc_start: 0.5813 (m100) cc_final: 0.4951 (m100) outliers start: 133 outliers final: 94 residues processed: 454 average time/residue: 0.2001 time to fit residues: 148.5565 Evaluate side-chains 426 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 314 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 660 ASN 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 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 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 396 GLU 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 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 170 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 281 TYR 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 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 696 ASN 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 104 HIS 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 442 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 650 HIS Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 20 LEU 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 162 LEU Chi-restraints excluded: chain E residue 295 VAL 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 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 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR 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 48 VAL Chi-restraints excluded: chain I residue 67 ARG 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 317 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 171 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 269 optimal weight: 6.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.118481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081675 restraints weight = 79157.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081889 restraints weight = 48398.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082042 restraints weight = 32605.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.082322 restraints weight = 31304.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082557 restraints weight = 27174.636| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32012 Z= 0.104 Angle : 0.521 10.367 43388 Z= 0.269 Chirality : 0.040 0.194 4903 Planarity : 0.003 0.052 5371 Dihedral : 5.250 68.644 4230 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.54 % Allowed : 17.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.14), residues: 3759 helix: 0.54 (0.13), residues: 1686 sheet: -0.28 (0.22), residues: 615 loop : -0.47 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 31 TYR 0.039 0.001 TYR D 325 PHE 0.026 0.001 PHE F 41 TRP 0.015 0.001 TRP D 647 HIS 0.008 0.001 HIS D 119 Details of bonding type rmsd covalent geometry : bond 0.00231 (31992) covalent geometry : angle 0.52078 (43348) SS BOND : bond 0.00265 ( 20) SS BOND : angle 0.63400 ( 40) hydrogen bonds : bond 0.03246 ( 1482) hydrogen bonds : angle 4.05390 ( 3882) *********************** 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 457 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 334 time to evaluate : 1.507 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: 0.8974 (OUTLIER) cc_final: 0.8212 (t70) REVERT: A 154 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: A 238 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8057 (mm-30) REVERT: A 426 ASP cc_start: 0.7307 (t0) cc_final: 0.7095 (t0) REVERT: A 516 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6929 (tptp) REVERT: A 540 LEU cc_start: 0.8959 (tp) cc_final: 0.8708 (tp) REVERT: A 687 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 733 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 115 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7814 (tp30) REVERT: B 226 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6508 (mmm-85) REVERT: B 244 PHE cc_start: 0.6536 (OUTLIER) cc_final: 0.5468 (m-80) REVERT: B 265 MET cc_start: 0.7122 (tpp) cc_final: 0.6908 (tpp) REVERT: B 434 MET cc_start: 0.6680 (mmp) cc_final: 0.6243 (mtp) REVERT: B 444 ASP cc_start: 0.7768 (t70) cc_final: 0.7482 (t0) REVERT: B 506 LYS cc_start: 0.8360 (pttm) cc_final: 0.7774 (tmtt) REVERT: B 590 MET cc_start: 0.8401 (mmm) cc_final: 0.7926 (mmm) REVERT: B 689 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7620 (m-80) REVERT: B 721 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: B 791 PHE cc_start: 0.6735 (t80) cc_final: 0.6230 (t80) REVERT: C 245 GLU cc_start: 0.8037 (pt0) cc_final: 0.7829 (tp30) REVERT: C 281 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8784 (p90) REVERT: C 353 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6557 (t80) REVERT: C 377 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6888 (m170) REVERT: C 405 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7491 (mm) REVERT: C 422 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6794 (mmmm) REVERT: C 429 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6454 (pm20) REVERT: C 471 LEU cc_start: 0.8159 (tp) cc_final: 0.7882 (tp) REVERT: C 590 MET cc_start: 0.5882 (mmp) cc_final: 0.5630 (mmp) REVERT: D 104 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7911 (t70) REVERT: D 135 ILE cc_start: 0.8785 (tt) cc_final: 0.8380 (mt) REVERT: D 218 ARG cc_start: 0.7247 (ttt180) cc_final: 0.6949 (tmt170) REVERT: D 235 LYS cc_start: 0.7801 (mttt) cc_final: 0.7585 (ptpt) REVERT: D 434 MET cc_start: 0.7848 (mmm) cc_final: 0.7334 (mmm) REVERT: D 446 VAL cc_start: 0.7913 (m) cc_final: 0.7273 (p) REVERT: D 454 GLU cc_start: 0.7471 (tt0) cc_final: 0.7037 (tp30) REVERT: D 459 VAL cc_start: 0.6706 (OUTLIER) cc_final: 0.6418 (p) REVERT: D 467 GLN cc_start: 0.6998 (mt0) cc_final: 0.6681 (tm-30) REVERT: D 555 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6525 (mt) REVERT: D 571 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8257 (ttmm) REVERT: D 588 LYS cc_start: 0.7962 (ptpt) cc_final: 0.7733 (pttm) REVERT: D 592 ASN cc_start: 0.7892 (m-40) cc_final: 0.7353 (t0) REVERT: D 686 LYS cc_start: 0.7660 (mttp) cc_final: 0.6976 (mmmm) REVERT: E 46 GLN cc_start: 0.8578 (tp40) cc_final: 0.7820 (tm-30) REVERT: E 49 GLN cc_start: 0.7394 (mm-40) cc_final: 0.6918 (mm-40) REVERT: E 112 ASN cc_start: 0.8767 (m-40) cc_final: 0.8561 (m-40) REVERT: E 117 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7662 (tp30) REVERT: E 157 HIS cc_start: 0.5416 (m170) cc_final: 0.5205 (m170) REVERT: E 248 PHE cc_start: 0.7011 (t80) cc_final: 0.6527 (t80) REVERT: E 348 GLU cc_start: 0.5284 (mt-10) cc_final: 0.5029 (pm20) REVERT: F 44 THR cc_start: 0.8396 (m) cc_final: 0.8026 (p) REVERT: F 156 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.5632 (tm-30) REVERT: F 280 ASN cc_start: 0.6848 (m-40) cc_final: 0.6386 (m110) REVERT: F 300 MET cc_start: 0.8266 (tpp) cc_final: 0.7937 (mmp) REVERT: F 314 HIS cc_start: 0.7253 (t70) cc_final: 0.6882 (t-90) REVERT: F 330 TYR cc_start: 0.5585 (t80) cc_final: 0.5334 (t80) REVERT: G 34 MET cc_start: 0.8029 (mmt) cc_final: 0.7619 (mmt) REVERT: G 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8440 (tp30) REVERT: G 56 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7753 (mp0) REVERT: G 107 GLN cc_start: 0.6692 (mm-40) cc_final: 0.6183 (pm20) REVERT: H 34 MET cc_start: 0.7318 (mmt) cc_final: 0.6621 (ttm) REVERT: I 32 HIS cc_start: 0.5080 (OUTLIER) cc_final: 0.3695 (m-70) REVERT: I 74 ASN cc_start: 0.5941 (m-40) cc_final: 0.4906 (p0) REVERT: J 36 TRP cc_start: 0.5760 (m100) cc_final: 0.4915 (m100) outliers start: 123 outliers final: 95 residues processed: 437 average time/residue: 0.1927 time to fit residues: 139.6615 Evaluate side-chains 432 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 319 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 170 THR Chi-restraints excluded: chain A residue 231 VAL 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 727 LEU Chi-restraints excluded: chain A residue 733 LEU 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 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 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 368 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 396 GLU 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 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 40 VAL 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 281 TYR 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 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 696 ASN 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 104 HIS 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 555 LEU Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 767 GLU Chi-restraints excluded: chain E residue 20 LEU 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 162 LEU Chi-restraints excluded: chain E residue 295 VAL 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 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 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR 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 48 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 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 63 optimal weight: 0.8980 chunk 361 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 238 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 243 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 121 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 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 = 0.3982 r_free = 0.3982 target = 0.117836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081467 restraints weight = 79652.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081431 restraints weight = 49921.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081542 restraints weight = 33934.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081834 restraints weight = 34631.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082148 restraints weight = 28169.822| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 32012 Z= 0.128 Angle : 0.536 14.268 43388 Z= 0.277 Chirality : 0.041 0.190 4903 Planarity : 0.003 0.052 5371 Dihedral : 5.294 70.296 4230 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.46 % Allowed : 17.48 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.14), residues: 3759 helix: 0.54 (0.13), residues: 1674 sheet: -0.30 (0.22), residues: 615 loop : -0.44 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 31 TYR 0.041 0.001 TYR D 325 PHE 0.026 0.001 PHE F 41 TRP 0.012 0.001 TRP D 647 HIS 0.008 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00294 (31992) covalent geometry : angle 0.53626 (43348) SS BOND : bond 0.00278 ( 20) SS BOND : angle 0.61378 ( 40) hydrogen bonds : bond 0.03351 ( 1482) hydrogen bonds : angle 4.06868 ( 3882) ********************** 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 440 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 320 time to evaluate : 1.343 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: symmetry clash REVERT: A 104 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8167 (t70) REVERT: A 154 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: A 238 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 426 ASP cc_start: 0.7304 (t0) cc_final: 0.7095 (t0) REVERT: A 516 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6945 (tptp) REVERT: A 540 LEU cc_start: 0.8973 (tp) cc_final: 0.8723 (tp) REVERT: A 687 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8402 (mt) REVERT: A 708 GLN cc_start: 0.7201 (mp10) cc_final: 0.6931 (mm110) REVERT: A 733 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7706 (mp) REVERT: B 115 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7883 (tp30) REVERT: B 226 ARG cc_start: 0.6970 (mtp85) cc_final: 0.6533 (mmm-85) REVERT: B 244 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.5587 (m-80) REVERT: B 434 MET cc_start: 0.6669 (mmp) cc_final: 0.6233 (mtp) REVERT: B 444 ASP cc_start: 0.7834 (t70) cc_final: 0.7555 (t0) REVERT: B 448 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8771 (tp) REVERT: B 506 LYS cc_start: 0.8334 (pttm) cc_final: 0.7756 (tmtt) REVERT: B 590 MET cc_start: 0.8396 (mmm) cc_final: 0.7915 (mmm) REVERT: B 689 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: B 721 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6527 (pt0) REVERT: C 281 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.8738 (p90) REVERT: C 353 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6598 (t80) REVERT: C 377 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.6916 (m170) REVERT: C 405 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7490 (mm) REVERT: C 422 LYS cc_start: 0.7151 (mtpt) cc_final: 0.6816 (mmmm) REVERT: C 471 LEU cc_start: 0.8234 (tp) cc_final: 0.7958 (tp) REVERT: C 590 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5668 (mmp) REVERT: C 597 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7974 (mp0) REVERT: C 688 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7493 (mtm-85) REVERT: D 104 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7974 (t70) REVERT: D 135 ILE cc_start: 0.8821 (tt) cc_final: 0.8432 (mt) REVERT: D 218 ARG cc_start: 0.7265 (ttt180) cc_final: 0.6969 (tmt170) REVERT: D 235 LYS cc_start: 0.7806 (mttt) cc_final: 0.7594 (ptpt) REVERT: D 434 MET cc_start: 0.7856 (mmm) cc_final: 0.7340 (mmm) REVERT: D 446 VAL cc_start: 0.7972 (m) cc_final: 0.7331 (p) REVERT: D 454 GLU cc_start: 0.7508 (tt0) cc_final: 0.7104 (tp30) REVERT: D 459 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6428 (p) REVERT: D 467 GLN cc_start: 0.7025 (mt0) cc_final: 0.6685 (tm-30) REVERT: D 555 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6609 (mt) REVERT: D 571 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8386 (ttmm) REVERT: D 588 LYS cc_start: 0.7985 (ptpt) cc_final: 0.7769 (pttm) REVERT: D 592 ASN cc_start: 0.7855 (m-40) cc_final: 0.7295 (t0) REVERT: D 686 LYS cc_start: 0.7593 (mttp) cc_final: 0.6907 (mmmm) REVERT: E 46 GLN cc_start: 0.8602 (tp40) cc_final: 0.7758 (tm-30) REVERT: E 49 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6758 (mm-40) REVERT: E 112 ASN cc_start: 0.8860 (m-40) cc_final: 0.8618 (m-40) REVERT: E 117 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7895 (tp30) REVERT: E 248 PHE cc_start: 0.7109 (t80) cc_final: 0.6647 (t80) REVERT: E 348 GLU cc_start: 0.5353 (mt-10) cc_final: 0.5044 (pm20) REVERT: F 44 THR cc_start: 0.8452 (m) cc_final: 0.8063 (p) REVERT: F 114 MET cc_start: 0.8843 (mmm) cc_final: 0.8361 (tpt) REVERT: F 156 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5657 (tm-30) REVERT: F 280 ASN cc_start: 0.6877 (m-40) cc_final: 0.6386 (m110) REVERT: F 300 MET cc_start: 0.8310 (tpp) cc_final: 0.7939 (mmp) REVERT: F 309 ASN cc_start: 0.8388 (m-40) cc_final: 0.8039 (t0) REVERT: F 330 TYR cc_start: 0.5496 (t80) cc_final: 0.5209 (t80) REVERT: G 34 MET cc_start: 0.8061 (mmt) cc_final: 0.7664 (mmt) REVERT: G 46 GLU cc_start: 0.8849 (tt0) cc_final: 0.8411 (tp30) REVERT: G 56 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7755 (mp0) REVERT: H 34 MET cc_start: 0.7337 (mmt) cc_final: 0.6775 (ttt) REVERT: I 32 HIS cc_start: 0.5017 (OUTLIER) cc_final: 0.3632 (m-70) REVERT: I 67 ARG cc_start: 0.4990 (mmm-85) cc_final: 0.4585 (mmm-85) REVERT: I 74 ASN cc_start: 0.5961 (m-40) cc_final: 0.4920 (p0) REVERT: J 36 TRP cc_start: 0.5780 (m100) cc_final: 0.4937 (m100) REVERT: J 95 TYR cc_start: 0.6089 (m-80) cc_final: 0.5627 (m-80) outliers start: 120 outliers final: 96 residues processed: 421 average time/residue: 0.2004 time to fit residues: 139.0193 Evaluate side-chains 428 residues out of total 3474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 313 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 170 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 330 ILE 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 594 THR 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 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 286 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 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 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 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 40 VAL 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 281 TYR 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 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 590 MET 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 47 VAL Chi-restraints excluded: chain D residue 104 HIS 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 459 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 561 VAL 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 20 LEU 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 162 LEU Chi-restraints excluded: chain E residue 295 VAL 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 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 322 CYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 65 LYS Chi-restraints excluded: chain G residue 69 THR 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 48 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 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 345 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 286 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 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 = 0.3978 r_free = 0.3978 target = 0.117614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081290 restraints weight = 79955.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080479 restraints weight = 55313.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081008 restraints weight = 36545.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081623 restraints weight = 30554.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.081718 restraints weight = 27184.343| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32012 Z= 0.129 Angle : 0.541 11.006 43388 Z= 0.280 Chirality : 0.041 0.190 4903 Planarity : 0.003 0.051 5371 Dihedral : 5.317 70.425 4230 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.46 % Allowed : 17.71 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.14), residues: 3759 helix: 0.54 (0.13), residues: 1672 sheet: -0.30 (0.22), residues: 615 loop : -0.44 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 72 TYR 0.043 0.001 TYR D 325 PHE 0.026 0.001 PHE F 41 TRP 0.012 0.001 TRP D 647 HIS 0.008 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00296 (31992) covalent geometry : angle 0.54138 (43348) SS BOND : bond 0.00291 ( 20) SS BOND : angle 0.62579 ( 40) hydrogen bonds : bond 0.03373 ( 1482) hydrogen bonds : angle 4.07769 ( 3882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5897.53 seconds wall clock time: 103 minutes 13.58 seconds (6193.58 seconds total)