Starting phenix.real_space_refine on Fri Jun 5 16:22:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.map" model { file = "/net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rru_54204/06_2026/9rru_54204.cif" } resolution = 3.2 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= 0.032 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 120 5.16 5 C 14034 2.51 5 N 3571 2.21 5 O 3835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21564 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5392 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Chain breaks: 6 Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5392 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Chain breaks: 6 Chain: "C" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5392 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Chain breaks: 6 Chain: "D" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5384 Classifications: {'peptide': 661} Link IDs: {'PTRANS': 24, 'TRANS': 636} Chain breaks: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1156 SG CYS A 176 53.089 106.774 76.078 1.00145.91 S ATOM 1170 SG CYS A 178 52.348 109.268 76.725 1.00162.07 S ATOM 6548 SG CYS B 176 107.489 76.290 76.149 1.00161.11 S ATOM 6584 SG CYS B 181 107.366 72.683 78.449 1.00157.20 S ATOM 11940 SG CYS C 176 22.816 52.253 75.516 1.00168.60 S ATOM 11954 SG CYS C 178 19.560 51.828 76.976 1.00168.99 S ATOM 11976 SG CYS C 181 21.799 55.102 77.885 1.00162.45 S ATOM 17332 SG CYS D 176 75.617 21.784 76.856 1.00163.90 S ATOM 17368 SG CYS D 181 72.979 22.077 78.549 1.00159.73 S Time building chain proxies: 4.99, per 1000 atoms: 0.23 Number of scatterers: 21564 At special positions: 0 Unit cell: (128.232, 128.232, 140.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 120 16.00 O 3835 8.00 N 3571 7.00 C 14034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " 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: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 178 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 181 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 801 " - pdb=" SG CYS C 176 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 176 " 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5102 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 3 sheets defined 77.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.788A pdb=" N GLU A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.561A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.515A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.574A pdb=" N HIS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 removed outlier: 3.776A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.670A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.540A pdb=" N LYS A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.623A pdb=" N ILE A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.615A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.498A pdb=" N PHE A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.775A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 420 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 433 through 460 removed outlier: 3.670A pdb=" N LEU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP A 439 " --> pdb=" O TRP A 435 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.543A pdb=" N TRP A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.115A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.654A pdb=" N GLY A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.762A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 626 removed outlier: 3.735A pdb=" N MET A 623 " --> pdb=" O MET A 619 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 658 through 662 Processing helix chain 'A' and resid 707 through 735 removed outlier: 3.500A pdb=" N ARG A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 762 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.892A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 157 through 164 removed outlier: 3.509A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 3.703A pdb=" N GLU B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.513A pdb=" N ALA B 252 " --> pdb=" O CYS B 248 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.511A pdb=" N ILE B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.573A pdb=" N GLN B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.557A pdb=" N CYS B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.627A pdb=" N SER B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 removed outlier: 4.363A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 362' Processing helix chain 'B' and resid 362 through 387 removed outlier: 4.296A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 420 removed outlier: 3.612A pdb=" N MET B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 433 through 460 removed outlier: 4.196A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.574A pdb=" N ILE B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.044A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 540 removed outlier: 4.387A pdb=" N LEU B 506 " --> pdb=" O HIS B 502 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.918A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 616 through 629 removed outlier: 4.608A pdb=" N ASN B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER B 627 " --> pdb=" O MET B 623 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 628 " --> pdb=" O MET B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 649 Processing helix chain 'B' and resid 658 through 663 removed outlier: 4.145A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 736 Processing helix chain 'B' and resid 739 through 763 removed outlier: 3.502A pdb=" N PHE B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 756 " --> pdb=" O SER B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.691A pdb=" N ALA C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.774A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.833A pdb=" N TYR C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.664A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.515A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.510A pdb=" N ILE C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.720A pdb=" N LEU C 349 " --> pdb=" O SER C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 387 removed outlier: 4.189A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 Proline residue: C 409 - end of helix removed outlier: 3.518A pdb=" N GLY C 413 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 removed outlier: 3.654A pdb=" N SER C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 removed outlier: 3.557A pdb=" N ILE C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.876A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 540 removed outlier: 3.879A pdb=" N LEU C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 585 through 589 Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 630 removed outlier: 3.734A pdb=" N ILE C 621 " --> pdb=" O LEU C 617 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 622 " --> pdb=" O ASN C 618 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 627 " --> pdb=" O MET C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 650 removed outlier: 3.818A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 6.228A pdb=" N GLY C 654 " --> pdb=" O PHE C 651 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY C 655 " --> pdb=" O ASP C 652 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 656 " --> pdb=" O GLU C 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 651 through 656' Processing helix chain 'C' and resid 658 through 663 removed outlier: 4.184A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 736 Processing helix chain 'C' and resid 739 through 763 removed outlier: 3.629A pdb=" N PHE C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 44 through 59 removed outlier: 4.243A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.657A pdb=" N ALA D 77 " --> pdb=" O ALA D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.656A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.602A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.714A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 removed outlier: 3.554A pdb=" N LEU D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 340 removed outlier: 4.363A pdb=" N THR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.624A pdb=" N TYR D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 362 removed outlier: 4.133A pdb=" N ILE D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 361 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 362' Processing helix chain 'D' and resid 362 through 383 Processing helix chain 'D' and resid 401 through 421 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 434 through 460 removed outlier: 3.908A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 440 " --> pdb=" O ASN D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.507A pdb=" N GLU D 468 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 492 removed outlier: 3.548A pdb=" N ALA D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.755A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 540 removed outlier: 3.972A pdb=" N LEU D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE D 520 " --> pdb=" O ASP D 516 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.515A pdb=" N CYS D 553 " --> pdb=" O PRO D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.678A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 627 removed outlier: 3.869A pdb=" N ASN D 625 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 652 removed outlier: 4.013A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP D 652 " --> pdb=" O MET D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'D' and resid 707 through 736 removed outlier: 3.587A pdb=" N GLU D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 763 removed outlier: 3.555A pdb=" N LEU D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 763 " --> pdb=" O ASP D 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.849A pdb=" N VAL A 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 167 through 169 1372 hydrogen bonds defined for protein. 4002 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: 3.90 Time building geometry restraints manager: 2.22 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: 6793 1.34 - 1.46: 5292 1.46 - 1.58: 9775 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 22056 Sorted by residual: bond pdb=" CA THR A 336 " pdb=" CB THR A 336 " ideal model delta sigma weight residual 1.530 1.558 -0.028 1.69e-02 3.50e+03 2.76e+00 bond pdb=" CB GLU A 240 " pdb=" CG GLU A 240 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CB GLU D 479 " pdb=" CG GLU D 479 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" CB GLU C 240 " pdb=" CG GLU C 240 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CG LYS A 34 " pdb=" CD LYS A 34 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.32e+00 ... (remaining 22051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 29738 3.17 - 6.34: 122 6.34 - 9.51: 19 9.51 - 12.67: 1 12.67 - 15.84: 1 Bond angle restraints: 29881 Sorted by residual: angle pdb=" C MET A 335 " pdb=" N THR A 336 " pdb=" CA THR A 336 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C CYS B 178 " pdb=" N VAL B 179 " pdb=" CA VAL B 179 " ideal model delta sigma weight residual 121.97 128.50 -6.53 1.80e+00 3.09e-01 1.32e+01 angle pdb=" CA ILE B 350 " pdb=" CB ILE B 350 " pdb=" CG1 ILE B 350 " ideal model delta sigma weight residual 110.40 116.45 -6.05 1.70e+00 3.46e-01 1.27e+01 angle pdb=" CA VAL C 96 " pdb=" CB VAL C 96 " pdb=" CG1 VAL C 96 " ideal model delta sigma weight residual 110.40 116.19 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" CB GLU A 240 " pdb=" CG GLU A 240 " pdb=" CD GLU A 240 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.70e+00 3.46e-01 1.12e+01 ... (remaining 29876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11002 17.92 - 35.84: 1531 35.84 - 53.76: 533 53.76 - 71.67: 93 71.67 - 89.59: 29 Dihedral angle restraints: 13188 sinusoidal: 5359 harmonic: 7829 Sorted by residual: dihedral pdb=" CB CYS A 553 " pdb=" SG CYS A 553 " pdb=" SG CYS A 558 " pdb=" CB CYS A 558 " ideal model delta sinusoidal sigma weight residual -86.00 -130.39 44.39 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA GLN A 163 " pdb=" C GLN A 163 " pdb=" N LYS A 164 " pdb=" CA LYS A 164 " ideal model delta harmonic sigma weight residual 180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP C 434 " pdb=" C TRP C 434 " pdb=" N TRP C 435 " pdb=" CA TRP C 435 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 13185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2680 0.044 - 0.088: 589 0.088 - 0.132: 103 0.132 - 0.176: 9 0.176 - 0.219: 1 Chirality restraints: 3382 Sorted by residual: chirality pdb=" CB VAL B 179 " pdb=" CA VAL B 179 " pdb=" CG1 VAL B 179 " pdb=" CG2 VAL B 179 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C 96 " pdb=" CA VAL C 96 " pdb=" CG1 VAL C 96 " pdb=" CG2 VAL C 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA THR A 336 " pdb=" N THR A 336 " pdb=" C THR A 336 " pdb=" CB THR A 336 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 3379 not shown) Planarity restraints: 3727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 397 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 398 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 398 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 398 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 351 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO A 352 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 67 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO D 68 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO D 68 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 68 " -0.028 5.00e-02 4.00e+02 ... (remaining 3724 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 9725 2.97 - 3.45: 22705 3.45 - 3.93: 35469 3.93 - 4.42: 40935 4.42 - 4.90: 65520 Nonbonded interactions: 174354 Sorted by model distance: nonbonded pdb=" N GLU A 240 " pdb=" OE1 GLU A 240 " model vdw 2.486 3.120 nonbonded pdb=" O CYS B 178 " pdb="ZN ZN B 801 " model vdw 2.514 2.230 nonbonded pdb=" O ASN A 551 " pdb=" OD1 ASN A 551 " model vdw 2.515 3.040 nonbonded pdb=" CB CYS D 178 " pdb="ZN ZN D 801 " model vdw 2.528 2.630 nonbonded pdb=" N GLU C 240 " pdb=" OE1 GLU C 240 " model vdw 2.560 3.120 ... (remaining 174349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 629 or resid 634 through 801)) selection = (chain 'B' and (resid 16 through 629 or resid 634 through 801)) selection = (chain 'C' and (resid 16 through 629 or resid 634 through 801)) selection = chain 'D' } 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 individual isotropic 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: 8.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.060 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 0.044 22070 Z= 0.102 Angle : 0.546 15.843 29887 Z= 0.265 Chirality : 0.037 0.219 3382 Planarity : 0.004 0.054 3727 Dihedral : 18.841 89.592 8077 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.55 % Favored : 97.41 % Rotamer: Outliers : 0.63 % Allowed : 35.61 % Favored : 63.75 % 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 are not related in a simple way. whole: -0.27 (0.16), residues: 2591 helix: -0.01 (0.11), residues: 1866 sheet: None (None), residues: 0 loop : -0.23 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 71 TYR 0.018 0.001 TYR B 541 PHE 0.016 0.001 PHE B 540 TRP 0.013 0.001 TRP C 327 HIS 0.003 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (22056) covalent geometry : angle 0.54577 / 0.26 (29881) SS BOND : bond 0.00082 / 0.04 ( 3) SS BOND : angle 1.07277 / 0.60 ( 6) hydrogen bonds : bond 0.25127 / 16.77 ( 1372) hydrogen bonds : angle 7.17799 / 5.01 ( 4002) metal coordination : bond 0.00569 / 0.26 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 544 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8012 (mp0) cc_final: 0.7728 (mp0) REVERT: A 44 ASP cc_start: 0.8292 (t0) cc_final: 0.7929 (t0) REVERT: A 53 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7923 (mm-40) REVERT: A 156 GLU cc_start: 0.8247 (tt0) cc_final: 0.7991 (tt0) REVERT: A 439 ASP cc_start: 0.7493 (m-30) cc_final: 0.7177 (m-30) REVERT: A 570 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: A 711 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7687 (tp40) REVERT: B 81 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 266 GLU cc_start: 0.7567 (pp20) cc_final: 0.7332 (pp20) REVERT: B 361 LYS cc_start: 0.8435 (mttt) cc_final: 0.8116 (mmtp) REVERT: B 541 TYR cc_start: 0.8306 (m-80) cc_final: 0.7692 (m-80) REVERT: C 196 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7877 (ttt-90) REVERT: C 214 GLU cc_start: 0.8645 (tp30) cc_final: 0.7998 (mp0) REVERT: C 335 MET cc_start: 0.7560 (mmm) cc_final: 0.7241 (mmm) REVERT: C 406 MET cc_start: 0.5916 (mmp) cc_final: 0.5544 (mmt) REVERT: C 512 ARG cc_start: 0.8571 (tpm170) cc_final: 0.7736 (ttm170) REVERT: C 513 MET cc_start: 0.8457 (mtm) cc_final: 0.8137 (mtp) REVERT: C 591 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7786 (mppt) REVERT: C 709 GLN cc_start: 0.8159 (tp40) cc_final: 0.7881 (tp40) REVERT: C 747 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8484 (mtpp) REVERT: D 49 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7973 (ttpp) REVERT: D 84 GLU cc_start: 0.8586 (mp0) cc_final: 0.7927 (mp0) REVERT: D 188 ASP cc_start: 0.8054 (t0) cc_final: 0.7756 (t70) REVERT: D 266 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7372 (tt0) REVERT: D 396 GLN cc_start: 0.8048 (mt0) cc_final: 0.7686 (mt0) REVERT: D 471 MET cc_start: 0.7505 (ptp) cc_final: 0.7004 (ptt) REVERT: D 559 GLU cc_start: 0.8597 (tt0) cc_final: 0.8230 (mm-30) REVERT: D 618 ASN cc_start: 0.8257 (t0) cc_final: 0.7948 (t0) REVERT: D 634 HIS cc_start: 0.5667 (t-90) cc_final: 0.5098 (t70) REVERT: D 638 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7256 (mp0) REVERT: D 715 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 740 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7397 (tt0) outliers start: 15 outliers final: 10 residues processed: 552 average time/residue: 0.1646 time to fit residues: 137.1242 Evaluate side-chains 537 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 525 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 748 GLN Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 533 ASN A 551 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN C 443 ASN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103603 restraints weight = 25861.813| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.90 r_work: 0.2919 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22070 Z= 0.228 Angle : 0.619 16.055 29887 Z= 0.318 Chirality : 0.042 0.168 3382 Planarity : 0.005 0.057 3727 Dihedral : 4.983 48.762 2869 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 5.41 % Allowed : 29.74 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2591 helix: 1.07 (0.12), residues: 1890 sheet: None (None), residues: 0 loop : -0.19 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 754 TYR 0.016 0.001 TYR D 118 PHE 0.015 0.002 PHE D 341 TRP 0.015 0.001 TRP C 434 HIS 0.004 0.001 HIS C 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (22056) covalent geometry : angle 0.61931 / 0.32 (29881) SS BOND : bond 0.00266 / 0.14 ( 3) SS BOND : angle 0.67345 / 0.38 ( 6) hydrogen bonds : bond 0.06197 / 4.11 ( 1372) hydrogen bonds : angle 4.38794 / 3.10 ( 4002) metal coordination : bond 0.00362 / 0.20 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 564 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8372 (t0) cc_final: 0.7783 (t0) REVERT: A 53 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8158 (mm-40) REVERT: A 173 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 242 GLU cc_start: 0.8382 (tp30) cc_final: 0.8163 (tp30) REVERT: A 243 GLU cc_start: 0.8188 (mp0) cc_final: 0.7795 (mp0) REVERT: A 343 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6660 (mpt) REVERT: A 507 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: A 754 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8130 (ttt-90) REVERT: B 28 GLU cc_start: 0.7450 (pm20) cc_final: 0.6634 (pm20) REVERT: B 81 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 84 GLU cc_start: 0.8323 (mp0) cc_final: 0.8113 (mp0) REVERT: B 194 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7992 (tpt170) REVERT: B 266 GLU cc_start: 0.8154 (pp20) cc_final: 0.7916 (pp20) REVERT: B 361 LYS cc_start: 0.8584 (mttt) cc_final: 0.8342 (mmtp) REVERT: B 431 ILE cc_start: 0.1228 (OUTLIER) cc_final: 0.0999 (mm) REVERT: B 503 LEU cc_start: 0.8990 (mm) cc_final: 0.8774 (mt) REVERT: B 545 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7177 (mtm-85) REVERT: C 65 CYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 66 MET cc_start: 0.8144 (mtp) cc_final: 0.7493 (mmt) REVERT: C 71 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7922 (mtm-85) REVERT: C 335 MET cc_start: 0.7852 (mmm) cc_final: 0.7551 (mmm) REVERT: C 386 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.4597 (mm-40) REVERT: C 406 MET cc_start: 0.6296 (mmp) cc_final: 0.5965 (mmt) REVERT: C 446 TYR cc_start: 0.8460 (m-80) cc_final: 0.8156 (m-80) REVERT: C 512 ARG cc_start: 0.8727 (tpm170) cc_final: 0.8038 (ttm170) REVERT: C 513 MET cc_start: 0.8484 (mtm) cc_final: 0.8201 (mtp) REVERT: C 519 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8008 (mmtm) REVERT: C 591 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8058 (mppt) REVERT: D 21 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: D 49 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8410 (ttpp) REVERT: D 79 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: D 84 GLU cc_start: 0.8685 (mp0) cc_final: 0.8149 (mp0) REVERT: D 164 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.6673 (mppt) REVERT: D 170 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8212 (ttp-170) REVERT: D 266 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7885 (tt0) REVERT: D 471 MET cc_start: 0.7574 (ptp) cc_final: 0.7247 (ptt) REVERT: D 507 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: D 559 GLU cc_start: 0.8661 (tt0) cc_final: 0.8284 (mm-30) REVERT: D 595 GLU cc_start: 0.8364 (mp0) cc_final: 0.7647 (mm-30) REVERT: D 618 ASN cc_start: 0.8647 (t0) cc_final: 0.8394 (t0) REVERT: D 715 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 740 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7117 (tt0) outliers start: 128 outliers final: 64 residues processed: 638 average time/residue: 0.1616 time to fit residues: 156.4472 Evaluate side-chains 623 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 544 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 748 GLN Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 740 GLU Chi-restraints excluded: chain D residue 757 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 223 optimal weight: 0.5980 chunk 142 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 252 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 306 ASN ** B 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 ASN D 163 GLN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 742 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106210 restraints weight = 25555.406| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.94 r_work: 0.2965 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22070 Z= 0.145 Angle : 0.539 15.991 29887 Z= 0.274 Chirality : 0.039 0.171 3382 Planarity : 0.004 0.057 3727 Dihedral : 4.413 47.912 2859 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 4.99 % Allowed : 28.52 % Favored : 66.50 % 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 are not related in a simple way. whole: 1.64 (0.16), residues: 2591 helix: 1.57 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -0.15 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 754 TYR 0.010 0.001 TYR A 586 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP C 434 HIS 0.002 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (22056) covalent geometry : angle 0.53935 / 0.27 (29881) SS BOND : bond 0.00558 / 0.29 ( 3) SS BOND : angle 0.71474 / 0.40 ( 6) hydrogen bonds : bond 0.05037 / 3.37 ( 1372) hydrogen bonds : angle 3.97932 / 2.81 ( 4002) metal coordination : bond 0.01604 / 0.84 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 581 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8248 (t0) cc_final: 0.7634 (t0) REVERT: A 53 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8254 (mm-40) REVERT: A 54 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 173 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 230 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 343 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6550 (mpt) REVERT: A 439 ASP cc_start: 0.7399 (m-30) cc_final: 0.7175 (m-30) REVERT: A 507 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: A 711 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: A 740 GLU cc_start: 0.8721 (tp30) cc_final: 0.8428 (mm-30) REVERT: A 748 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 754 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7728 (tmt-80) REVERT: B 81 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 194 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7964 (tpt170) REVERT: B 266 GLU cc_start: 0.8186 (pp20) cc_final: 0.7933 (pp20) REVERT: B 287 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 361 LYS cc_start: 0.8573 (mttt) cc_final: 0.8344 (mmtp) REVERT: B 431 ILE cc_start: 0.1126 (OUTLIER) cc_final: 0.0888 (mm) REVERT: B 503 LEU cc_start: 0.8969 (mm) cc_final: 0.8758 (mt) REVERT: B 513 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7283 (mpt) REVERT: B 545 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.6997 (mtm-85) REVERT: C 138 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8122 (tt0) REVERT: C 180 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: C 335 MET cc_start: 0.7866 (mmm) cc_final: 0.7565 (mmm) REVERT: C 404 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.4976 (mt-10) REVERT: C 406 MET cc_start: 0.6410 (mmp) cc_final: 0.5999 (mmt) REVERT: C 512 ARG cc_start: 0.8742 (tpm170) cc_final: 0.8102 (ttm170) REVERT: C 513 MET cc_start: 0.8484 (mtm) cc_final: 0.8209 (mtp) REVERT: C 519 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7940 (mmtm) REVERT: C 561 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.8881 (mt0) REVERT: C 591 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8052 (mppt) REVERT: D 49 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8382 (ttpp) REVERT: D 79 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: D 84 GLU cc_start: 0.8694 (mp0) cc_final: 0.8171 (mp0) REVERT: D 164 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6714 (mppt) REVERT: D 170 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8207 (ttp-170) REVERT: D 266 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7842 (tt0) REVERT: D 471 MET cc_start: 0.7583 (ptp) cc_final: 0.7233 (ptt) REVERT: D 507 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: D 559 GLU cc_start: 0.8598 (tt0) cc_final: 0.8239 (mm-30) REVERT: D 638 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8042 (mt-10) REVERT: D 715 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 759 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8300 (m-30) outliers start: 118 outliers final: 69 residues processed: 646 average time/residue: 0.1600 time to fit residues: 157.1454 Evaluate side-chains 644 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 556 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 748 GLN Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 221 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 259 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 537 GLN A 551 ASN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 ASN C 153 ASN C 306 ASN C 629 GLN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN D 742 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107075 restraints weight = 25458.157| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.94 r_work: 0.2969 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22070 Z= 0.129 Angle : 0.526 15.854 29887 Z= 0.266 Chirality : 0.038 0.149 3382 Planarity : 0.004 0.055 3727 Dihedral : 4.225 47.683 2857 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 5.83 % Allowed : 28.22 % Favored : 65.95 % 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 are not related in a simple way. whole: 1.97 (0.16), residues: 2591 helix: 1.84 (0.12), residues: 1901 sheet: None (None), residues: 0 loop : -0.13 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 754 TYR 0.010 0.001 TYR A 586 PHE 0.018 0.001 PHE A 341 TRP 0.014 0.001 TRP C 434 HIS 0.002 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22056) covalent geometry : angle 0.52635 / 0.27 (29881) SS BOND : bond 0.00549 / 0.29 ( 3) SS BOND : angle 0.73005 / 0.42 ( 6) hydrogen bonds : bond 0.04445 / 2.97 ( 1372) hydrogen bonds : angle 3.78161 / 2.67 ( 4002) metal coordination : bond 0.00631 / 0.31 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 592 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8241 (mp0) cc_final: 0.8038 (mp0) REVERT: A 44 ASP cc_start: 0.8262 (t0) cc_final: 0.7701 (t0) REVERT: A 53 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8258 (mm-40) REVERT: A 54 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7336 (tm-30) REVERT: A 82 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8172 (t0) REVERT: A 173 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: A 230 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8222 (mp) REVERT: A 343 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6449 (mpt) REVERT: A 439 ASP cc_start: 0.7378 (m-30) cc_final: 0.7115 (m-30) REVERT: A 507 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 570 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: A 711 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: A 740 GLU cc_start: 0.8705 (tp30) cc_final: 0.8415 (mm-30) REVERT: A 748 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 754 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7667 (tmt-80) REVERT: B 81 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 194 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7923 (tpt170) REVERT: B 228 LYS cc_start: 0.8896 (tttt) cc_final: 0.8558 (tttt) REVERT: B 266 GLU cc_start: 0.8173 (pp20) cc_final: 0.7935 (pp20) REVERT: B 287 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8251 (mt) REVERT: B 361 LYS cc_start: 0.8555 (mttt) cc_final: 0.8336 (mmtp) REVERT: B 431 ILE cc_start: 0.1003 (OUTLIER) cc_final: 0.0776 (mm) REVERT: B 513 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (mpt) REVERT: C 66 MET cc_start: 0.8059 (mtp) cc_final: 0.7434 (mmt) REVERT: C 138 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8143 (tt0) REVERT: C 165 ARG cc_start: 0.7200 (mmm160) cc_final: 0.6852 (tpm170) REVERT: C 180 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: C 335 MET cc_start: 0.7892 (mmm) cc_final: 0.7583 (mmm) REVERT: C 386 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.4559 (mt0) REVERT: C 404 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.4980 (mt-10) REVERT: C 406 MET cc_start: 0.6399 (mmp) cc_final: 0.6009 (mmt) REVERT: C 415 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7418 (mp) REVERT: C 512 ARG cc_start: 0.8762 (tpm170) cc_final: 0.8156 (ttm170) REVERT: C 513 MET cc_start: 0.8448 (mtm) cc_final: 0.8170 (mtp) REVERT: C 519 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7980 (mmtm) REVERT: C 561 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8740 (mt0) REVERT: C 591 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8044 (mppt) REVERT: D 21 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: D 84 GLU cc_start: 0.8697 (mp0) cc_final: 0.8176 (mp0) REVERT: D 114 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8326 (tp) REVERT: D 164 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.6844 (mppt) REVERT: D 266 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7818 (tt0) REVERT: D 471 MET cc_start: 0.7558 (ptp) cc_final: 0.7136 (ptt) REVERT: D 492 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8634 (tpt90) REVERT: D 507 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: D 559 GLU cc_start: 0.8617 (tt0) cc_final: 0.8267 (mm-30) REVERT: D 629 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.6019 (pt0) REVERT: D 662 ASN cc_start: 0.6672 (m-40) cc_final: 0.6461 (m110) REVERT: D 715 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7612 (mm-30) REVERT: D 759 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8265 (m-30) outliers start: 138 outliers final: 75 residues processed: 671 average time/residue: 0.1584 time to fit residues: 162.2119 Evaluate side-chains 667 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 568 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105545 restraints weight = 25533.648| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.93 r_work: 0.2950 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22070 Z= 0.166 Angle : 0.545 15.758 29887 Z= 0.275 Chirality : 0.039 0.266 3382 Planarity : 0.004 0.064 3727 Dihedral : 4.175 48.373 2854 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 5.83 % Allowed : 28.22 % Favored : 65.95 % 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 are not related in a simple way. whole: 2.01 (0.16), residues: 2591 helix: 1.88 (0.12), residues: 1905 sheet: None (None), residues: 0 loop : -0.16 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 754 TYR 0.010 0.001 TYR A 586 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP C 434 HIS 0.003 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (22056) covalent geometry : angle 0.54532 / 0.27 (29881) SS BOND : bond 0.00042 / 0.02 ( 3) SS BOND : angle 1.00039 / 0.57 ( 6) hydrogen bonds : bond 0.04564 / 3.05 ( 1372) hydrogen bonds : angle 3.76387 / 2.65 ( 4002) metal coordination : bond 0.00469 / 0.24 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 578 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8349 (t0) cc_final: 0.7724 (t0) REVERT: A 53 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8289 (mm-40) REVERT: A 54 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7321 (tm-30) REVERT: A 82 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 173 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: A 230 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8322 (mp) REVERT: A 253 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8532 (ttpp) REVERT: A 343 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6423 (mpt) REVERT: A 439 ASP cc_start: 0.7398 (m-30) cc_final: 0.7080 (m-30) REVERT: A 507 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: A 570 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: A 711 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: A 738 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 740 GLU cc_start: 0.8696 (tp30) cc_final: 0.8364 (mm-30) REVERT: A 748 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 754 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7659 (tmt-80) REVERT: B 56 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 81 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 194 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7933 (tpt-90) REVERT: B 228 LYS cc_start: 0.8886 (tttt) cc_final: 0.8565 (tttt) REVERT: B 266 GLU cc_start: 0.8169 (pp20) cc_final: 0.7941 (pp20) REVERT: B 287 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8289 (mt) REVERT: B 361 LYS cc_start: 0.8569 (mttt) cc_final: 0.8348 (mmtp) REVERT: B 431 ILE cc_start: 0.0974 (OUTLIER) cc_final: 0.0770 (mm) REVERT: B 479 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 513 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7354 (mpt) REVERT: C 66 MET cc_start: 0.8073 (mtp) cc_final: 0.7446 (mmt) REVERT: C 138 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8116 (tt0) REVERT: C 165 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6852 (tpm170) REVERT: C 180 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5817 (tt0) REVERT: C 335 MET cc_start: 0.7880 (mmm) cc_final: 0.7566 (mmm) REVERT: C 386 GLN cc_start: 0.5885 (OUTLIER) cc_final: 0.4688 (mt0) REVERT: C 404 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4867 (mt-10) REVERT: C 406 MET cc_start: 0.6417 (mmp) cc_final: 0.6014 (mmt) REVERT: C 512 ARG cc_start: 0.8756 (tpm170) cc_final: 0.8127 (ttm170) REVERT: C 513 MET cc_start: 0.8446 (mtm) cc_final: 0.8075 (mtp) REVERT: C 519 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7849 (mmtt) REVERT: C 561 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8962 (mt0) REVERT: C 591 LYS cc_start: 0.8490 (mmmt) cc_final: 0.7996 (mppt) REVERT: C 617 LEU cc_start: 0.8516 (tt) cc_final: 0.7794 (mm) REVERT: D 21 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: D 71 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7039 (ptm-80) REVERT: D 79 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: D 84 GLU cc_start: 0.8711 (mp0) cc_final: 0.8182 (mp0) REVERT: D 114 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8328 (tp) REVERT: D 164 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6879 (mppt) REVERT: D 170 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8201 (ttp-170) REVERT: D 266 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7821 (tt0) REVERT: D 471 MET cc_start: 0.7511 (ptp) cc_final: 0.7157 (ptt) REVERT: D 492 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8584 (tpt90) REVERT: D 507 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: D 559 GLU cc_start: 0.8625 (tt0) cc_final: 0.8230 (mm-30) REVERT: D 560 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8177 (tptm) REVERT: D 629 GLN cc_start: 0.6284 (OUTLIER) cc_final: 0.5985 (pt0) REVERT: D 662 ASN cc_start: 0.6665 (m-40) cc_final: 0.6455 (m110) REVERT: D 715 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 759 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8287 (m-30) outliers start: 138 outliers final: 85 residues processed: 653 average time/residue: 0.1600 time to fit residues: 159.5115 Evaluate side-chains 681 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 568 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 257 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.106367 restraints weight = 25514.615| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.94 r_work: 0.2961 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22070 Z= 0.145 Angle : 0.539 15.803 29887 Z= 0.270 Chirality : 0.039 0.190 3382 Planarity : 0.004 0.064 3727 Dihedral : 4.151 48.887 2854 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 5.62 % Allowed : 28.01 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2591 helix: 1.97 (0.12), residues: 1905 sheet: None (None), residues: 0 loop : -0.13 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 754 TYR 0.011 0.001 TYR C 348 PHE 0.017 0.001 PHE A 341 TRP 0.014 0.001 TRP C 434 HIS 0.002 0.000 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (22056) covalent geometry : angle 0.53920 / 0.27 (29881) SS BOND : bond 0.00228 / 0.12 ( 3) SS BOND : angle 0.80543 / 0.46 ( 6) hydrogen bonds : bond 0.04348 / 2.90 ( 1372) hydrogen bonds : angle 3.69877 / 2.60 ( 4002) metal coordination : bond 0.00402 / 0.20 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 571 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7940 (pt0) REVERT: A 44 ASP cc_start: 0.8329 (t0) cc_final: 0.7715 (t0) REVERT: A 53 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8297 (mm-40) REVERT: A 58 TYR cc_start: 0.6665 (m-80) cc_final: 0.6411 (m-80) REVERT: A 82 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8152 (t0) REVERT: A 173 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: A 230 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 253 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8520 (ttpp) REVERT: A 343 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6384 (mpt) REVERT: A 439 ASP cc_start: 0.7350 (m-30) cc_final: 0.7006 (m-30) REVERT: A 507 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: A 570 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: A 711 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: A 738 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 740 GLU cc_start: 0.8688 (tp30) cc_final: 0.8354 (mm-30) REVERT: A 748 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 754 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7688 (tmt-80) REVERT: B 56 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 194 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7714 (tpt-90) REVERT: B 228 LYS cc_start: 0.8893 (tttt) cc_final: 0.8627 (tttt) REVERT: B 266 GLU cc_start: 0.8169 (pp20) cc_final: 0.7940 (pp20) REVERT: B 287 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8278 (mt) REVERT: B 361 LYS cc_start: 0.8543 (mttt) cc_final: 0.8315 (mmtp) REVERT: B 431 ILE cc_start: 0.1173 (OUTLIER) cc_final: 0.0948 (mm) REVERT: B 513 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7210 (mpt) REVERT: B 733 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7988 (mtpp) REVERT: C 66 MET cc_start: 0.8109 (mtp) cc_final: 0.7473 (mmt) REVERT: C 138 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8119 (tt0) REVERT: C 165 ARG cc_start: 0.7196 (mmm160) cc_final: 0.6862 (tpm170) REVERT: C 180 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5801 (tt0) REVERT: C 214 GLU cc_start: 0.8785 (tp30) cc_final: 0.8311 (mp0) REVERT: C 230 LEU cc_start: 0.8246 (tp) cc_final: 0.7995 (tp) REVERT: C 335 MET cc_start: 0.7909 (mmm) cc_final: 0.7600 (mmm) REVERT: C 386 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.4664 (mt0) REVERT: C 404 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.4880 (mt-10) REVERT: C 406 MET cc_start: 0.6320 (mmp) cc_final: 0.5972 (mmt) REVERT: C 512 ARG cc_start: 0.8740 (tpm170) cc_final: 0.8127 (ttm170) REVERT: C 513 MET cc_start: 0.8392 (mtm) cc_final: 0.8035 (mtp) REVERT: C 519 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7832 (mmtt) REVERT: C 561 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8642 (mt0) REVERT: C 591 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7967 (mppt) REVERT: C 617 LEU cc_start: 0.8535 (tt) cc_final: 0.7828 (mm) REVERT: C 709 GLN cc_start: 0.7726 (tp40) cc_final: 0.7399 (tp40) REVERT: D 21 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: D 33 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 79 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: D 84 GLU cc_start: 0.8684 (mp0) cc_final: 0.8300 (mp0) REVERT: D 114 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8331 (tp) REVERT: D 164 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.6912 (mppt) REVERT: D 170 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8208 (ttp-170) REVERT: D 266 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7831 (tt0) REVERT: D 459 LYS cc_start: 0.7343 (mtpp) cc_final: 0.7137 (tttt) REVERT: D 471 MET cc_start: 0.7529 (ptp) cc_final: 0.7107 (ptt) REVERT: D 492 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8562 (tpt90) REVERT: D 559 GLU cc_start: 0.8611 (tt0) cc_final: 0.8385 (mt-10) REVERT: D 595 GLU cc_start: 0.8320 (mp0) cc_final: 0.7515 (mm-30) REVERT: D 629 GLN cc_start: 0.6221 (OUTLIER) cc_final: 0.5921 (pt0) REVERT: D 715 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 759 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8268 (m-30) outliers start: 133 outliers final: 84 residues processed: 636 average time/residue: 0.1601 time to fit residues: 154.6178 Evaluate side-chains 670 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 558 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 249 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 228 optimal weight: 5.9990 chunk 198 optimal weight: 0.0040 chunk 143 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN C 629 GLN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.137076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108014 restraints weight = 25440.406| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.94 r_work: 0.2982 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22070 Z= 0.118 Angle : 0.517 15.522 29887 Z= 0.259 Chirality : 0.037 0.166 3382 Planarity : 0.004 0.062 3727 Dihedral : 4.040 48.292 2854 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 5.37 % Allowed : 28.60 % Favored : 66.03 % 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 are not related in a simple way. whole: 2.30 (0.17), residues: 2591 helix: 2.11 (0.12), residues: 1905 sheet: None (None), residues: 0 loop : -0.07 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 754 TYR 0.012 0.001 TYR C 348 PHE 0.023 0.001 PHE A 377 TRP 0.014 0.001 TRP A 434 HIS 0.002 0.000 HIS B 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22056) covalent geometry : angle 0.51671 / 0.26 (29881) SS BOND : bond 0.00145 / 0.08 ( 3) SS BOND : angle 0.71863 / 0.41 ( 6) hydrogen bonds : bond 0.03973 / 2.66 ( 1372) hydrogen bonds : angle 3.60434 / 2.53 ( 4002) metal coordination : bond 0.00347 / 0.17 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 579 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: A 33 GLU cc_start: 0.8219 (mp0) cc_final: 0.7949 (pm20) REVERT: A 44 ASP cc_start: 0.8302 (t0) cc_final: 0.7690 (t0) REVERT: A 53 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8274 (mm-40) REVERT: A 58 TYR cc_start: 0.6699 (m-80) cc_final: 0.6445 (m-80) REVERT: A 82 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8115 (t0) REVERT: A 173 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: A 230 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 253 LYS cc_start: 0.8697 (tmmt) cc_final: 0.8483 (ttpp) REVERT: A 343 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6334 (mpt) REVERT: A 439 ASP cc_start: 0.7325 (m-30) cc_final: 0.6936 (m-30) REVERT: A 507 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: A 570 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 711 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: A 738 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 740 GLU cc_start: 0.8628 (tp30) cc_final: 0.8308 (mm-30) REVERT: A 748 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 754 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7684 (tmt-80) REVERT: B 56 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 194 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7899 (tpt170) REVERT: B 228 LYS cc_start: 0.8878 (tttt) cc_final: 0.8628 (tttt) REVERT: B 266 GLU cc_start: 0.8173 (pp20) cc_final: 0.7961 (pp20) REVERT: B 287 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 361 LYS cc_start: 0.8527 (mttt) cc_final: 0.8303 (mmtp) REVERT: B 513 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7170 (mpt) REVERT: B 541 TYR cc_start: 0.8480 (m-80) cc_final: 0.7919 (m-80) REVERT: C 66 MET cc_start: 0.8138 (mtp) cc_final: 0.7494 (mmt) REVERT: C 138 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8129 (tt0) REVERT: C 165 ARG cc_start: 0.7156 (mmm160) cc_final: 0.6912 (tpm170) REVERT: C 180 GLU cc_start: 0.6152 (OUTLIER) cc_final: 0.5769 (tt0) REVERT: C 335 MET cc_start: 0.7890 (mmm) cc_final: 0.7601 (mmm) REVERT: C 404 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.4885 (mt-10) REVERT: C 406 MET cc_start: 0.6210 (mmp) cc_final: 0.5905 (mmt) REVERT: C 415 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7466 (mp) REVERT: C 446 TYR cc_start: 0.8399 (m-80) cc_final: 0.8132 (m-80) REVERT: C 471 MET cc_start: 0.8400 (ttm) cc_final: 0.8161 (ttm) REVERT: C 512 ARG cc_start: 0.8723 (tpm170) cc_final: 0.8103 (ttm170) REVERT: C 513 MET cc_start: 0.8385 (mtm) cc_final: 0.8069 (mtp) REVERT: C 519 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7924 (mmtm) REVERT: C 561 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8692 (mt0) REVERT: C 591 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7960 (mppt) REVERT: C 709 GLN cc_start: 0.7663 (tp40) cc_final: 0.7347 (tp40) REVERT: D 21 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: D 33 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 79 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 84 GLU cc_start: 0.8678 (mp0) cc_final: 0.8300 (mp0) REVERT: D 164 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.6970 (mppt) REVERT: D 266 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7834 (tt0) REVERT: D 422 MET cc_start: 0.3249 (OUTLIER) cc_final: 0.2766 (ptm) REVERT: D 471 MET cc_start: 0.7516 (ptp) cc_final: 0.7110 (ptt) REVERT: D 492 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8601 (tpt90) REVERT: D 507 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: D 513 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7419 (mtt) REVERT: D 559 GLU cc_start: 0.8633 (tt0) cc_final: 0.8418 (mt-10) REVERT: D 595 GLU cc_start: 0.8298 (mp0) cc_final: 0.7513 (mm-30) REVERT: D 715 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7497 (mm-30) REVERT: D 759 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8251 (m-30) outliers start: 127 outliers final: 72 residues processed: 646 average time/residue: 0.1687 time to fit residues: 166.2690 Evaluate side-chains 657 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 559 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 545 ARG Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 621 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 551 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.134147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104681 restraints weight = 25518.049| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.01 r_work: 0.2929 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22070 Z= 0.206 Angle : 0.580 17.177 29887 Z= 0.292 Chirality : 0.040 0.306 3382 Planarity : 0.004 0.062 3727 Dihedral : 4.188 49.969 2852 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.84 % Rotamer: Outliers : 5.75 % Allowed : 28.43 % Favored : 65.82 % 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 are not related in a simple way. whole: 2.07 (0.17), residues: 2591 helix: 1.93 (0.12), residues: 1907 sheet: None (None), residues: 0 loop : -0.16 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 754 TYR 0.012 0.001 TYR D 118 PHE 0.017 0.002 PHE A 341 TRP 0.015 0.001 TRP C 434 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (22056) covalent geometry : angle 0.57948 / 0.29 (29881) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 1.01437 / 0.57 ( 6) hydrogen bonds : bond 0.04641 / 3.09 ( 1372) hydrogen bonds : angle 3.73417 / 2.63 ( 4002) metal coordination : bond 0.00402 / 0.21 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 568 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 33 GLU cc_start: 0.8298 (mp0) cc_final: 0.7926 (pm20) REVERT: A 44 ASP cc_start: 0.8415 (t0) cc_final: 0.7799 (t0) REVERT: A 53 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8285 (mm-40) REVERT: A 82 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 173 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: A 230 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 240 GLU cc_start: 0.7472 (mp0) cc_final: 0.6953 (mp0) REVERT: A 246 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8004 (tp40) REVERT: A 253 LYS cc_start: 0.8778 (tmmt) cc_final: 0.8554 (ttpp) REVERT: A 343 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6329 (mpt) REVERT: A 439 ASP cc_start: 0.7435 (m-30) cc_final: 0.7069 (m-30) REVERT: A 507 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: A 738 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7950 (mp) REVERT: A 740 GLU cc_start: 0.8719 (tp30) cc_final: 0.8412 (mm-30) REVERT: A 748 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 754 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7692 (tmt-80) REVERT: B 56 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 71 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8053 (mtp-110) REVERT: B 194 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7819 (tpt-90) REVERT: B 228 LYS cc_start: 0.8907 (tttt) cc_final: 0.8595 (tttt) REVERT: B 266 GLU cc_start: 0.8224 (pp20) cc_final: 0.8014 (pp20) REVERT: B 287 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8357 (mt) REVERT: B 361 LYS cc_start: 0.8515 (mttt) cc_final: 0.8279 (mmtp) REVERT: B 479 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7818 (mt-10) REVERT: B 513 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7280 (mpt) REVERT: B 541 TYR cc_start: 0.8577 (m-80) cc_final: 0.8053 (m-80) REVERT: C 66 MET cc_start: 0.8187 (mtp) cc_final: 0.7526 (mmt) REVERT: C 138 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8143 (tt0) REVERT: C 165 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6897 (tpm170) REVERT: C 214 GLU cc_start: 0.8732 (tp30) cc_final: 0.8320 (mp0) REVERT: C 335 MET cc_start: 0.7868 (mmm) cc_final: 0.7551 (mmm) REVERT: C 386 GLN cc_start: 0.5985 (OUTLIER) cc_final: 0.4816 (mt0) REVERT: C 404 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.4970 (mt-10) REVERT: C 406 MET cc_start: 0.6297 (mmp) cc_final: 0.5969 (mmt) REVERT: C 415 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7580 (mp) REVERT: C 512 ARG cc_start: 0.8731 (tpm170) cc_final: 0.8068 (ttm170) REVERT: C 519 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7830 (mmtt) REVERT: C 591 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8005 (mppt) REVERT: C 709 GLN cc_start: 0.7793 (tp40) cc_final: 0.7475 (tt0) REVERT: C 730 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7404 (tpt-90) REVERT: D 21 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: D 33 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 71 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6997 (ptm-80) REVERT: D 79 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: D 84 GLU cc_start: 0.8694 (mp0) cc_final: 0.8308 (mp0) REVERT: D 164 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6920 (mppt) REVERT: D 170 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8230 (ttp-170) REVERT: D 266 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7854 (tt0) REVERT: D 336 THR cc_start: 0.8144 (m) cc_final: 0.7938 (m) REVERT: D 471 MET cc_start: 0.7583 (ptp) cc_final: 0.7086 (ptt) REVERT: D 492 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8672 (tpt90) REVERT: D 507 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: D 559 GLU cc_start: 0.8651 (tt0) cc_final: 0.8406 (mt-10) REVERT: D 560 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8226 (tptm) REVERT: D 595 GLU cc_start: 0.8344 (mp0) cc_final: 0.7543 (mm-30) REVERT: D 629 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5873 (pt0) REVERT: D 715 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7619 (mm-30) REVERT: D 759 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8326 (m-30) outliers start: 136 outliers final: 94 residues processed: 639 average time/residue: 0.1653 time to fit residues: 160.3488 Evaluate side-chains 671 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 550 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 562 ASN Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 730 ARG Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 554 LYS Chi-restraints excluded: chain D residue 560 LYS Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 126 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 258 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 198 optimal weight: 0.0170 chunk 5 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 ASN ** D 662 ASN ** 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 = 0.3480 r_free = 0.3480 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107725 restraints weight = 25346.455| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.11 r_work: 0.2957 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22070 Z= 0.134 Angle : 0.548 16.686 29887 Z= 0.274 Chirality : 0.038 0.157 3382 Planarity : 0.004 0.063 3727 Dihedral : 4.130 50.124 2852 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 4.86 % Allowed : 29.40 % Favored : 65.74 % 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 are not related in a simple way. whole: 2.19 (0.17), residues: 2591 helix: 2.03 (0.12), residues: 1907 sheet: None (None), residues: 0 loop : -0.13 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 754 TYR 0.010 0.001 TYR C 348 PHE 0.019 0.001 PHE A 377 TRP 0.015 0.001 TRP A 434 HIS 0.002 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (22056) covalent geometry : angle 0.54791 / 0.27 (29881) SS BOND : bond 0.00144 / 0.08 ( 3) SS BOND : angle 1.01736 / 0.58 ( 6) hydrogen bonds : bond 0.04144 / 2.77 ( 1372) hydrogen bonds : angle 3.64114 / 2.56 ( 4002) metal coordination : bond 0.00310 / 0.16 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 554 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: A 33 GLU cc_start: 0.8228 (mp0) cc_final: 0.7846 (pm20) REVERT: A 44 ASP cc_start: 0.8335 (t0) cc_final: 0.7692 (t0) REVERT: A 53 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8261 (mm-40) REVERT: A 82 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8101 (t0) REVERT: A 173 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 230 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 240 GLU cc_start: 0.7329 (mp0) cc_final: 0.6812 (mp0) REVERT: A 246 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7938 (tp40) REVERT: A 253 LYS cc_start: 0.8639 (tmmt) cc_final: 0.8387 (ttpp) REVERT: A 343 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6253 (mpt) REVERT: A 405 TRP cc_start: 0.7295 (m100) cc_final: 0.6657 (m100) REVERT: A 439 ASP cc_start: 0.7344 (m-30) cc_final: 0.6919 (m-30) REVERT: A 507 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: A 738 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 740 GLU cc_start: 0.8661 (tp30) cc_final: 0.8355 (mm-30) REVERT: A 748 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 754 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7599 (tmt-80) REVERT: B 56 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 71 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7976 (mtp-110) REVERT: B 194 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7941 (tpt170) REVERT: B 228 LYS cc_start: 0.8848 (tttt) cc_final: 0.8598 (tttt) REVERT: B 266 GLU cc_start: 0.8105 (pp20) cc_final: 0.7871 (pp20) REVERT: B 287 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 361 LYS cc_start: 0.8456 (mttt) cc_final: 0.8212 (mmtp) REVERT: B 513 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7159 (mpt) REVERT: B 541 TYR cc_start: 0.8551 (m-80) cc_final: 0.7920 (m-80) REVERT: B 733 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7813 (mtpp) REVERT: C 66 MET cc_start: 0.8219 (mtp) cc_final: 0.7520 (mmt) REVERT: C 165 ARG cc_start: 0.7205 (mmm160) cc_final: 0.6910 (tpm170) REVERT: C 214 GLU cc_start: 0.8709 (tp30) cc_final: 0.8246 (mp0) REVERT: C 335 MET cc_start: 0.7831 (mmm) cc_final: 0.7486 (mmm) REVERT: C 404 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.4814 (mt-10) REVERT: C 406 MET cc_start: 0.6118 (mmp) cc_final: 0.5835 (mmt) REVERT: C 415 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7412 (mp) REVERT: C 512 ARG cc_start: 0.8705 (tpm170) cc_final: 0.8006 (ttm170) REVERT: C 561 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8727 (mt0) REVERT: C 591 LYS cc_start: 0.8495 (mmmt) cc_final: 0.7961 (mppt) REVERT: D 21 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: D 33 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7453 (mm-30) REVERT: D 79 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: D 84 GLU cc_start: 0.8699 (mp0) cc_final: 0.8293 (mp0) REVERT: D 164 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6897 (mppt) REVERT: D 266 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7779 (tt0) REVERT: D 396 GLN cc_start: 0.8261 (mt0) cc_final: 0.7966 (mt0) REVERT: D 422 MET cc_start: 0.3169 (OUTLIER) cc_final: 0.2627 (ptm) REVERT: D 459 LYS cc_start: 0.7313 (mtpp) cc_final: 0.7064 (tttt) REVERT: D 471 MET cc_start: 0.7578 (ptp) cc_final: 0.7121 (ptt) REVERT: D 507 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: D 559 GLU cc_start: 0.8678 (tt0) cc_final: 0.8469 (mt-10) REVERT: D 595 GLU cc_start: 0.8298 (mp0) cc_final: 0.7465 (mm-30) REVERT: D 629 GLN cc_start: 0.6137 (OUTLIER) cc_final: 0.5827 (pt0) REVERT: D 715 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7510 (mm-30) REVERT: D 759 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8305 (m-30) outliers start: 115 outliers final: 83 residues processed: 612 average time/residue: 0.1579 time to fit residues: 147.1943 Evaluate side-chains 657 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 551 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 626 ASN Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 0.5980 chunk 263 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 202 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.135525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105777 restraints weight = 25623.920| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.10 r_work: 0.2921 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22070 Z= 0.206 Angle : 0.586 16.755 29887 Z= 0.294 Chirality : 0.040 0.203 3382 Planarity : 0.004 0.066 3727 Dihedral : 4.160 51.390 2850 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 5.11 % Allowed : 29.02 % Favored : 65.86 % 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 are not related in a simple way. whole: 2.01 (0.17), residues: 2591 helix: 1.91 (0.12), residues: 1905 sheet: None (None), residues: 0 loop : -0.24 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 754 TYR 0.012 0.001 TYR C 348 PHE 0.019 0.002 PHE A 377 TRP 0.017 0.001 TRP A 434 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (22056) covalent geometry : angle 0.58614 / 0.29 (29881) SS BOND : bond 0.00194 / 0.10 ( 3) SS BOND : angle 1.12636 / 0.63 ( 6) hydrogen bonds : bond 0.04602 / 3.06 ( 1372) hydrogen bonds : angle 3.73446 / 2.62 ( 4002) metal coordination : bond 0.00382 / 0.20 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 550 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: A 33 GLU cc_start: 0.8279 (mp0) cc_final: 0.7871 (pm20) REVERT: A 44 ASP cc_start: 0.8384 (t0) cc_final: 0.7739 (t0) REVERT: A 53 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 82 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 173 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: A 230 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8316 (mp) REVERT: A 240 GLU cc_start: 0.7459 (mp0) cc_final: 0.6922 (mp0) REVERT: A 246 GLN cc_start: 0.8443 (mm-40) cc_final: 0.7948 (tp40) REVERT: A 253 LYS cc_start: 0.8726 (tmmt) cc_final: 0.8498 (ttpp) REVERT: A 343 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6278 (mpt) REVERT: A 405 TRP cc_start: 0.7329 (m100) cc_final: 0.6697 (m100) REVERT: A 439 ASP cc_start: 0.7457 (m-30) cc_final: 0.7009 (m-30) REVERT: A 507 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: A 738 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 740 GLU cc_start: 0.8704 (tp30) cc_final: 0.8389 (mm-30) REVERT: A 748 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 754 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7596 (tmt-80) REVERT: B 56 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7098 (tm-30) REVERT: B 71 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8035 (mtp-110) REVERT: B 194 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8000 (tpt-90) REVERT: B 228 LYS cc_start: 0.8884 (tttt) cc_final: 0.8600 (tttt) REVERT: B 266 GLU cc_start: 0.8135 (pp20) cc_final: 0.7895 (pp20) REVERT: B 287 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 361 LYS cc_start: 0.8505 (mttt) cc_final: 0.8253 (mmtp) REVERT: B 479 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 513 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7260 (mpt) REVERT: B 541 TYR cc_start: 0.8564 (m-80) cc_final: 0.8021 (m-80) REVERT: B 733 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7873 (mtpp) REVERT: B 749 ASP cc_start: 0.8806 (t0) cc_final: 0.8594 (t0) REVERT: C 66 MET cc_start: 0.8239 (mtp) cc_final: 0.7537 (mmt) REVERT: C 138 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8176 (tt0) REVERT: C 165 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6875 (tpm170) REVERT: C 214 GLU cc_start: 0.8729 (tp30) cc_final: 0.8265 (mp0) REVERT: C 335 MET cc_start: 0.7826 (mmm) cc_final: 0.7493 (mmm) REVERT: C 386 GLN cc_start: 0.5957 (OUTLIER) cc_final: 0.4819 (mt0) REVERT: C 404 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.4874 (mt-10) REVERT: C 406 MET cc_start: 0.6289 (mmp) cc_final: 0.5955 (mmt) REVERT: C 415 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 512 ARG cc_start: 0.8718 (tpm170) cc_final: 0.8010 (ttm170) REVERT: C 519 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7794 (mmtt) REVERT: C 561 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8968 (mt0) REVERT: C 591 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7959 (mppt) REVERT: C 624 MET cc_start: 0.7619 (mtm) cc_final: 0.7344 (mtm) REVERT: D 21 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: D 79 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: D 84 GLU cc_start: 0.8706 (mp0) cc_final: 0.8162 (mp0) REVERT: D 164 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6937 (mppt) REVERT: D 232 LYS cc_start: 0.8532 (mttm) cc_final: 0.8126 (mtmm) REVERT: D 266 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7787 (tt0) REVERT: D 438 MET cc_start: 0.7776 (ttm) cc_final: 0.7498 (ttm) REVERT: D 471 MET cc_start: 0.7592 (ptp) cc_final: 0.7067 (ptt) REVERT: D 486 ASN cc_start: 0.8759 (m-40) cc_final: 0.8527 (m-40) REVERT: D 507 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: D 559 GLU cc_start: 0.8703 (tt0) cc_final: 0.8471 (mt-10) REVERT: D 595 GLU cc_start: 0.8310 (mp0) cc_final: 0.7464 (mm-30) REVERT: D 629 GLN cc_start: 0.6204 (OUTLIER) cc_final: 0.5902 (pt0) REVERT: D 715 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7562 (mm-30) REVERT: D 759 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8368 (m-30) outliers start: 121 outliers final: 88 residues processed: 614 average time/residue: 0.1676 time to fit residues: 155.5825 Evaluate side-chains 655 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 543 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 194 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 733 LYS Chi-restraints excluded: chain B residue 756 GLU Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 386 GLN Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 164 LYS Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 450 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 507 GLN Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 758 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 26 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 192 optimal weight: 0.0570 chunk 6 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 662 ASN ** 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 = 0.3461 r_free = 0.3461 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.106250 restraints weight = 25493.814| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.13 r_work: 0.2950 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22070 Z= 0.137 Angle : 0.557 16.743 29887 Z= 0.278 Chirality : 0.038 0.192 3382 Planarity : 0.004 0.064 3727 Dihedral : 4.097 51.486 2850 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.74 % Favored : 97.22 % Rotamer: Outliers : 4.65 % Allowed : 29.53 % Favored : 65.82 % 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 are not related in a simple way. whole: 2.16 (0.17), residues: 2591 helix: 2.02 (0.12), residues: 1905 sheet: None (None), residues: 0 loop : -0.19 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 754 TYR 0.020 0.001 TYR C 446 PHE 0.021 0.001 PHE A 377 TRP 0.016 0.001 TRP A 434 HIS 0.002 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22056) covalent geometry : angle 0.55643 / 0.28 (29881) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 1.40248 / 0.78 ( 6) hydrogen bonds : bond 0.04193 / 2.80 ( 1372) hydrogen bonds : angle 3.65194 / 2.56 ( 4002) metal coordination : bond 0.00312 / 0.16 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6373.06 seconds wall clock time: 109 minutes 39.79 seconds (6579.79 seconds total)