Starting phenix.real_space_refine on Fri Sep 19 01:47:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zr1_6941/09_2025/5zr1_6941.map" } resolution = 3.0 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 90 5.49 5 Mg 3 5.21 5 S 94 5.16 5 C 14012 2.51 5 N 3732 2.21 5 O 4329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22260 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3958 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 484} Chain breaks: 3 Chain: "B" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3041 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4822 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 566} Chain breaks: 1 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "E" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3758 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 21, 'TRANS': 438} Chain breaks: 1 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1335 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 831 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.98, per 1000 atoms: 0.22 Number of scatterers: 22260 At special positions: 0 Unit cell: (110.46, 129.396, 181.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 90 15.00 Mg 3 11.99 O 4329 8.00 N 3732 7.00 C 14012 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 743.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4862 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 13 sheets defined 57.5% alpha, 7.0% beta 41 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.720A pdb=" N LYS A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 378 " --> pdb=" O PHE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.016A pdb=" N GLU A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.725A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.572A pdb=" N LEU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.047A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 4.029A pdb=" N GLU A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.638A pdb=" N PHE A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 618 removed outlier: 3.607A pdb=" N THR A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 641 removed outlier: 3.755A pdb=" N LYS A 641 " --> pdb=" O LEU A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'A' and resid 685 through 698 removed outlier: 3.548A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 726 removed outlier: 3.879A pdb=" N ALA A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.589A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.607A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.920A pdb=" N GLU A 844 " --> pdb=" O LYS A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.581A pdb=" N PHE A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 851 " --> pdb=" O LYS A 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 851' Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.641A pdb=" N ALA A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.558A pdb=" N ARG A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 908 through 914' Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.616A pdb=" N ARG B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.788A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 332 removed outlier: 3.523A pdb=" N GLU B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.558A pdb=" N LYS B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.543A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.572A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.685A pdb=" N TRP B 465 " --> pdb=" O PRO B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.565A pdb=" N TYR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 513 " --> pdb=" O GLY B 509 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.568A pdb=" N MET B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 556 through 566 removed outlier: 3.680A pdb=" N HIS B 561 " --> pdb=" O LYS B 557 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 4.334A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 616 removed outlier: 3.762A pdb=" N VAL B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 92 removed outlier: 3.510A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.945A pdb=" N GLU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.779A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.617A pdb=" N PHE C 274 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 275 " --> pdb=" O LYS C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.529A pdb=" N THR C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 306 removed outlier: 3.650A pdb=" N PHE C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 332 removed outlier: 3.568A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.886A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 4.209A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 removed outlier: 4.123A pdb=" N SER C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 374 through 381 Processing helix chain 'C' and resid 386 through 393 removed outlier: 3.642A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 416 removed outlier: 3.608A pdb=" N LYS C 407 " --> pdb=" O ASN C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.559A pdb=" N ASN C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 515 removed outlier: 4.108A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.791A pdb=" N LYS C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.528A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 removed outlier: 3.620A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 585 removed outlier: 3.590A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 594 removed outlier: 3.808A pdb=" N GLU C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 59 removed outlier: 3.686A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 88 removed outlier: 3.607A pdb=" N GLU D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.657A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.062A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 removed outlier: 3.519A pdb=" N ILE D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.583A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.934A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.684A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 removed outlier: 3.852A pdb=" N ILE D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 359 " --> pdb=" O CYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.800A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.530A pdb=" N LEU D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.656A pdb=" N ARG D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.860A pdb=" N LYS D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.508A pdb=" N ALA D 484 " --> pdb=" O ASN D 480 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 497 removed outlier: 3.819A pdb=" N MET D 496 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.911A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.544A pdb=" N ASN E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.837A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.850A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 87 " --> pdb=" O TYR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.597A pdb=" N VAL E 102 " --> pdb=" O PRO E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.643A pdb=" N VAL E 109 " --> pdb=" O PRO E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 145 through 150 removed outlier: 3.550A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 175 through 183 removed outlier: 3.554A pdb=" N ARG E 178 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER E 180 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR E 181 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS E 182 " --> pdb=" O TYR E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 206 removed outlier: 3.522A pdb=" N CYS E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 212 through 222 removed outlier: 3.803A pdb=" N ILE E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 6.104A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 3.716A pdb=" N ASP E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 271 removed outlier: 3.773A pdb=" N SER E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.586A pdb=" N ILE E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 279' Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.709A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 292 Processing helix chain 'E' and resid 325 through 339 removed outlier: 3.676A pdb=" N TYR E 330 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.692A pdb=" N ILE E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.536A pdb=" N LEU E 386 " --> pdb=" O ALA E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.189A pdb=" N LEU E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.835A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.670A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.575A pdb=" N PHE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.964A pdb=" N CYS F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 310 removed outlier: 3.593A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 4.019A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 removed outlier: 4.182A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 354 removed outlier: 4.167A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 removed outlier: 3.618A pdb=" N VAL F 369 " --> pdb=" O CYS F 365 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 386 Processing helix chain 'F' and resid 393 through 403 removed outlier: 4.401A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 400 " --> pdb=" O GLU F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 430 removed outlier: 3.509A pdb=" N MET F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.322A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 473 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA A 597 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 475 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR A 474 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.554A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL A 773 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ARG A 683 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA5, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.228A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 131 removed outlier: 3.976A pdb=" N ASN C 103 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.794A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.373A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 98 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N THR D 251 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU D 100 " --> pdb=" O THR D 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.507A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 433 through 435 849 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6999 1.35 - 1.50: 6994 1.50 - 1.65: 8721 1.65 - 1.80: 104 1.80 - 1.94: 51 Bond restraints: 22869 Sorted by residual: bond pdb=" O2A AGS A2001 " pdb=" PA AGS A2001 " ideal model delta sigma weight residual 1.531 1.465 0.066 1.60e-02 3.91e+03 1.68e+01 bond pdb=" O2B AGS E2001 " pdb=" PB AGS E2001 " ideal model delta sigma weight residual 1.531 1.466 0.065 1.60e-02 3.91e+03 1.65e+01 bond pdb=" N LYS C 603 " pdb=" CA LYS C 603 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.23e-02 6.61e+03 1.45e+01 bond pdb=" O2A AGS E2001 " pdb=" PA AGS E2001 " ideal model delta sigma weight residual 1.531 1.472 0.059 1.60e-02 3.91e+03 1.35e+01 bond pdb=" N ASP F 390 " pdb=" CA ASP F 390 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.23e+00 ... (remaining 22864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 31048 4.42 - 8.85: 196 8.85 - 13.27: 22 13.27 - 17.70: 2 17.70 - 22.12: 1 Bond angle restraints: 31269 Sorted by residual: angle pdb=" CA LEU D 372 " pdb=" CB LEU D 372 " pdb=" CG LEU D 372 " ideal model delta sigma weight residual 116.30 138.42 -22.12 3.50e+00 8.16e-02 3.99e+01 angle pdb=" CA GLU E 370 " pdb=" CB GLU E 370 " pdb=" CG GLU E 370 " ideal model delta sigma weight residual 114.10 126.37 -12.27 2.00e+00 2.50e-01 3.76e+01 angle pdb=" CA LYS C 603 " pdb=" CB LYS C 603 " pdb=" CG LYS C 603 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" N THR B 242 " pdb=" CA THR B 242 " pdb=" C THR B 242 " ideal model delta sigma weight residual 110.80 101.07 9.73 2.13e+00 2.20e-01 2.09e+01 angle pdb=" C TYR B 473 " pdb=" N ASN B 474 " pdb=" CA ASN B 474 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 ... (remaining 31264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.81: 12928 28.81 - 57.62: 717 57.62 - 86.44: 53 86.44 - 115.25: 0 115.25 - 144.06: 2 Dihedral angle restraints: 13700 sinusoidal: 6240 harmonic: 7460 Sorted by residual: dihedral pdb=" CA LEU E 171 " pdb=" C LEU E 171 " pdb=" N GLU E 172 " pdb=" CA GLU E 172 " ideal model delta harmonic sigma weight residual -180.00 -140.93 -39.07 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA THR D 66 " pdb=" C THR D 66 " pdb=" N ASP D 67 " pdb=" CA ASP D 67 " ideal model delta harmonic sigma weight residual 180.00 141.97 38.03 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA ASP B 241 " pdb=" C ASP B 241 " pdb=" N THR B 242 " pdb=" CA THR B 242 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 13697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3257 0.098 - 0.196: 274 0.196 - 0.295: 12 0.295 - 0.393: 3 0.393 - 0.491: 1 Chirality restraints: 3547 Sorted by residual: chirality pdb=" PB AGS E2001 " pdb=" O2B AGS E2001 " pdb=" O3A AGS E2001 " pdb=" O3B AGS E2001 " both_signs ideal model delta sigma weight residual True 3.18 -2.69 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CB THR E 321 " pdb=" CA THR E 321 " pdb=" OG1 THR E 321 " pdb=" CG2 THR E 321 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA ASP F 390 " pdb=" N ASP F 390 " pdb=" C ASP F 390 " pdb=" CB ASP F 390 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3544 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 394 " 0.021 2.00e-02 2.50e+03 2.20e-02 8.43e+00 pdb=" CG PHE A 394 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 394 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 394 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 394 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 394 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 394 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 36 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" CD GLN E 36 " -0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN E 36 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 GLN E 36 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 371 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C VAL E 371 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL E 371 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN E 372 " 0.016 2.00e-02 2.50e+03 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 194 2.62 - 3.19: 17925 3.19 - 3.76: 35118 3.76 - 4.33: 50514 4.33 - 4.90: 79537 Nonbonded interactions: 183288 Sorted by model distance: nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D2002 " model vdw 2.050 2.170 nonbonded pdb=" O2G AGS D2001 " pdb="MG MG D2002 " model vdw 2.078 2.170 nonbonded pdb=" OG1 THR A 486 " pdb="MG MG A2002 " model vdw 2.110 2.170 nonbonded pdb=" O2B AGS A2001 " pdb="MG MG A2002 " model vdw 2.128 2.170 nonbonded pdb=" O3G AGS E2001 " pdb="MG MG E2002 " model vdw 2.145 2.170 ... (remaining 183283 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.630 Find NCS groups from input model: 0.150 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.007 0.071 22869 Z= 0.279 Angle : 1.040 22.122 31269 Z= 0.541 Chirality : 0.058 0.491 3547 Planarity : 0.006 0.067 3651 Dihedral : 15.723 144.062 8838 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.65 % Allowed : 4.43 % Favored : 94.92 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.12), residues: 2479 helix: -4.35 (0.06), residues: 1330 sheet: -1.74 (0.32), residues: 206 loop : -1.99 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 325 TYR 0.036 0.003 TYR B 304 PHE 0.050 0.004 PHE A 394 TRP 0.031 0.004 TRP B 305 HIS 0.022 0.003 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00656 (22869) covalent geometry : angle 1.04036 (31269) hydrogen bonds : bond 0.28171 ( 938) hydrogen bonds : angle 9.79636 ( 2639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 422 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8584 (mttm) cc_final: 0.8329 (mttm) REVERT: B 262 THR cc_start: 0.8249 (m) cc_final: 0.8020 (t) REVERT: B 362 ILE cc_start: 0.8398 (pt) cc_final: 0.8107 (pp) REVERT: B 557 LYS cc_start: 0.7895 (mttm) cc_final: 0.7617 (mtmm) REVERT: D 156 LYS cc_start: 0.8120 (mttt) cc_final: 0.7847 (mtpp) REVERT: D 218 GLU cc_start: 0.6897 (mp0) cc_final: 0.6696 (mm-30) REVERT: D 418 MET cc_start: 0.7915 (ttm) cc_final: 0.7332 (ttm) REVERT: D 465 GLN cc_start: 0.7539 (pt0) cc_final: 0.7327 (pt0) REVERT: E 245 GLN cc_start: 0.8271 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 298 ASN cc_start: 0.7208 (m-40) cc_final: 0.6486 (p0) REVERT: E 453 ASN cc_start: 0.8421 (p0) cc_final: 0.8150 (p0) REVERT: F 388 ASP cc_start: 0.7397 (t0) cc_final: 0.7007 (t0) outliers start: 15 outliers final: 3 residues processed: 433 average time/residue: 0.7162 time to fit residues: 351.2441 Evaluate side-chains 235 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 811 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 600 ASN A 787 ASN A 820 GLN A 836 ASN A 895 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 425 HIS B 426 ASN B 478 HIS B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 560 ASN C 62 HIS C 67 HIS C 190 ASN C 214 ASN C 239 ASN C 312 HIS C 313 ASN C 383 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN D 80 GLN D 105 GLN D 126 GLN D 137 HIS D 140 GLN D 233 ASN D 240 HIS D 279 GLN D 371 GLN D 458 ASN E 32 ASN ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 277 ASN E 377 GLN E 391 GLN E 422 GLN E 423 ASN F 383 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.155173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121297 restraints weight = 26575.413| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.97 r_work: 0.3023 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22869 Z= 0.174 Angle : 0.684 14.898 31269 Z= 0.363 Chirality : 0.045 0.198 3547 Planarity : 0.005 0.048 3651 Dihedral : 18.323 144.252 3725 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.56 % Allowed : 10.03 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.14), residues: 2479 helix: -2.17 (0.11), residues: 1325 sheet: -1.39 (0.33), residues: 203 loop : -1.70 (0.17), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 297 TYR 0.021 0.002 TYR B 304 PHE 0.022 0.002 PHE B 475 TRP 0.019 0.002 TRP B 305 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00402 (22869) covalent geometry : angle 0.68410 (31269) hydrogen bonds : bond 0.05556 ( 938) hydrogen bonds : angle 4.85283 ( 2639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 274 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8153 (mttm) cc_final: 0.7817 (mttm) REVERT: A 429 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8273 (tp40) REVERT: A 691 ILE cc_start: 0.8354 (tp) cc_final: 0.8033 (pt) REVERT: A 819 GLU cc_start: 0.8706 (pt0) cc_final: 0.8474 (tt0) REVERT: B 262 THR cc_start: 0.8400 (m) cc_final: 0.7917 (t) REVERT: B 270 THR cc_start: 0.7941 (m) cc_final: 0.7376 (p) REVERT: B 377 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: B 557 LYS cc_start: 0.7802 (mttm) cc_final: 0.7282 (mtmm) REVERT: C 411 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7058 (tmm-80) REVERT: D 117 SER cc_start: 0.8896 (m) cc_final: 0.8688 (m) REVERT: D 124 LYS cc_start: 0.8494 (tptm) cc_final: 0.8283 (tptm) REVERT: D 156 LYS cc_start: 0.8398 (mttt) cc_final: 0.7995 (mtpp) REVERT: D 295 ARG cc_start: 0.8213 (mmt90) cc_final: 0.7814 (mpt-90) REVERT: D 418 MET cc_start: 0.8321 (ttm) cc_final: 0.7844 (ttm) REVERT: D 465 GLN cc_start: 0.8506 (pt0) cc_final: 0.8200 (pt0) REVERT: D 517 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8524 (mp) REVERT: E 1 MET cc_start: 0.6167 (mmm) cc_final: 0.5901 (mmm) REVERT: E 245 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8401 (tm-30) REVERT: E 296 ASP cc_start: 0.7178 (m-30) cc_final: 0.6811 (p0) REVERT: E 298 ASN cc_start: 0.7883 (m-40) cc_final: 0.6602 (p0) REVERT: E 453 ASN cc_start: 0.8380 (p0) cc_final: 0.8052 (p0) REVERT: F 288 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8081 (tm) REVERT: F 344 HIS cc_start: 0.7173 (t-90) cc_final: 0.6759 (m90) REVERT: F 358 LYS cc_start: 0.7699 (pttm) cc_final: 0.7385 (pmtt) REVERT: F 376 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: F 387 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7973 (t70) REVERT: F 388 ASP cc_start: 0.8128 (t0) cc_final: 0.7695 (t0) outliers start: 82 outliers final: 23 residues processed: 330 average time/residue: 0.5866 time to fit residues: 222.9671 Evaluate side-chains 250 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 517 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 201 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 248 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 216 optimal weight: 0.0270 chunk 93 optimal weight: 0.1980 chunk 204 optimal weight: 0.1980 chunk 226 optimal weight: 0.8980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN B 310 GLN B 426 ASN B 493 GLN B 534 GLN B 538 ASN B 560 ASN C 53 ASN C 69 HIS C 241 ASN C 400 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS D 462 ASN ** E 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.158274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124658 restraints weight = 26581.208| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.98 r_work: 0.3059 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22869 Z= 0.116 Angle : 0.575 9.454 31269 Z= 0.306 Chirality : 0.041 0.175 3547 Planarity : 0.004 0.045 3651 Dihedral : 17.976 144.627 3723 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.26 % Allowed : 12.89 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 2479 helix: -0.86 (0.13), residues: 1319 sheet: -1.06 (0.35), residues: 202 loop : -1.46 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 344 TYR 0.017 0.001 TYR F 306 PHE 0.021 0.001 PHE C 589 TRP 0.012 0.001 TRP C 494 HIS 0.006 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00250 (22869) covalent geometry : angle 0.57489 (31269) hydrogen bonds : bond 0.04361 ( 938) hydrogen bonds : angle 4.24775 ( 2639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 268 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7780 (tp30) cc_final: 0.7366 (tp30) REVERT: A 425 LYS cc_start: 0.8119 (mttm) cc_final: 0.7749 (mttm) REVERT: A 449 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 819 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: B 270 THR cc_start: 0.7839 (m) cc_final: 0.7305 (p) REVERT: B 377 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8428 (mtmt) REVERT: B 524 MET cc_start: 0.8278 (ttm) cc_final: 0.7980 (ttp) REVERT: B 533 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7512 (mtt) REVERT: B 557 LYS cc_start: 0.7712 (mttm) cc_final: 0.7260 (mtmm) REVERT: B 568 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6860 (mp) REVERT: C 300 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: C 399 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7059 (mp0) REVERT: C 400 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6588 (p0) REVERT: C 411 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6950 (tmm-80) REVERT: C 515 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8178 (mttt) REVERT: C 592 GLU cc_start: 0.7947 (tt0) cc_final: 0.7703 (mt-10) REVERT: D 117 SER cc_start: 0.8951 (m) cc_final: 0.8737 (m) REVERT: D 124 LYS cc_start: 0.8386 (tptm) cc_final: 0.8135 (tptm) REVERT: D 156 LYS cc_start: 0.8353 (mttt) cc_final: 0.7946 (mtpp) REVERT: D 295 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7796 (mpt-90) REVERT: D 418 MET cc_start: 0.8356 (ttm) cc_final: 0.7864 (ttm) REVERT: D 465 GLN cc_start: 0.8412 (pt0) cc_final: 0.8168 (pt0) REVERT: E 1 MET cc_start: 0.5956 (mmm) cc_final: 0.5615 (mmm) REVERT: E 95 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7445 (p) REVERT: E 245 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8415 (tm-30) REVERT: E 274 THR cc_start: 0.3759 (OUTLIER) cc_final: 0.3318 (p) REVERT: E 296 ASP cc_start: 0.7119 (m-30) cc_final: 0.6806 (p0) REVERT: E 298 ASN cc_start: 0.7805 (m-40) cc_final: 0.6497 (p0) REVERT: E 341 LEU cc_start: 0.9011 (mm) cc_final: 0.8800 (mp) REVERT: E 344 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.7994 (ttt90) REVERT: E 424 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8841 (tp) REVERT: E 453 ASN cc_start: 0.8094 (p0) cc_final: 0.7882 (p0) REVERT: F 344 HIS cc_start: 0.7109 (t-90) cc_final: 0.6692 (m90) REVERT: F 354 MET cc_start: 0.7848 (mmt) cc_final: 0.7609 (tpt) REVERT: F 376 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: F 387 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7998 (t0) REVERT: F 388 ASP cc_start: 0.7912 (t0) cc_final: 0.7474 (t0) outliers start: 75 outliers final: 19 residues processed: 314 average time/residue: 0.5964 time to fit residues: 215.3827 Evaluate side-chains 257 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 424 LEU Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 61 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 608 GLN B 435 ASN B 472 ASN B 538 ASN B 560 ASN C 53 ASN C 241 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 400 ASN C 536 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 240 HIS D 323 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116065 restraints weight = 26518.051| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.02 r_work: 0.2946 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 22869 Z= 0.268 Angle : 0.700 11.478 31269 Z= 0.363 Chirality : 0.048 0.284 3547 Planarity : 0.004 0.049 3651 Dihedral : 18.293 165.338 3723 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.43 % Allowed : 13.45 % Favored : 82.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.16), residues: 2479 helix: -0.44 (0.14), residues: 1331 sheet: -1.01 (0.35), residues: 198 loop : -1.36 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 297 TYR 0.022 0.002 TYR B 304 PHE 0.023 0.002 PHE E 256 TRP 0.014 0.002 TRP B 305 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00654 (22869) covalent geometry : angle 0.69956 (31269) hydrogen bonds : bond 0.04796 ( 938) hydrogen bonds : angle 4.26729 ( 2639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 241 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8280 (mttm) cc_final: 0.8058 (mttm) REVERT: A 634 ASN cc_start: 0.8652 (m110) cc_final: 0.8364 (t0) REVERT: A 819 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: B 262 THR cc_start: 0.8347 (m) cc_final: 0.7934 (t) REVERT: B 270 THR cc_start: 0.7924 (m) cc_final: 0.7353 (p) REVERT: B 377 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8579 (mtmt) REVERT: B 384 VAL cc_start: 0.8518 (t) cc_final: 0.8270 (m) REVERT: B 536 MET cc_start: 0.8145 (mtp) cc_final: 0.7916 (mtm) REVERT: B 555 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 568 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7002 (mp) REVERT: B 572 GLU cc_start: 0.7478 (tp30) cc_final: 0.7244 (tm-30) REVERT: B 587 MET cc_start: 0.8544 (mtp) cc_final: 0.8323 (mtm) REVERT: C 201 MET cc_start: 0.9106 (mtm) cc_final: 0.8864 (mtm) REVERT: C 261 ARG cc_start: 0.8539 (mpt-90) cc_final: 0.8292 (mmt180) REVERT: C 399 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7013 (mp0) REVERT: C 411 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7075 (tmm160) REVERT: C 416 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7414 (mm-30) REVERT: C 471 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7152 (mtp85) REVERT: C 515 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8316 (mttt) REVERT: D 117 SER cc_start: 0.8971 (m) cc_final: 0.8767 (m) REVERT: D 156 LYS cc_start: 0.8504 (mttt) cc_final: 0.7932 (mtpp) REVERT: D 295 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7722 (mpt-90) REVERT: D 418 MET cc_start: 0.8352 (ttm) cc_final: 0.7868 (ttm) REVERT: D 465 GLN cc_start: 0.8563 (pt0) cc_final: 0.8286 (pt0) REVERT: E 1 MET cc_start: 0.6040 (mmm) cc_final: 0.5758 (mmm) REVERT: E 56 ASN cc_start: 0.8869 (p0) cc_final: 0.8639 (p0) REVERT: E 103 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (mt-10) REVERT: E 245 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8503 (tm-30) REVERT: E 274 THR cc_start: 0.3587 (OUTLIER) cc_final: 0.3123 (p) REVERT: E 296 ASP cc_start: 0.7173 (m-30) cc_final: 0.6848 (p0) REVERT: E 298 ASN cc_start: 0.7949 (m-40) cc_final: 0.6662 (p0) REVERT: E 341 LEU cc_start: 0.9108 (mm) cc_final: 0.8903 (mp) REVERT: E 344 ARG cc_start: 0.8360 (ttp-110) cc_final: 0.8001 (ttt90) REVERT: E 453 ASN cc_start: 0.8596 (p0) cc_final: 0.8194 (p0) REVERT: F 344 HIS cc_start: 0.7021 (t-90) cc_final: 0.6538 (m90) REVERT: F 354 MET cc_start: 0.7751 (mmt) cc_final: 0.7497 (mmm) REVERT: F 376 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: F 387 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7958 (t70) REVERT: F 388 ASP cc_start: 0.8018 (t0) cc_final: 0.7713 (t0) outliers start: 102 outliers final: 46 residues processed: 315 average time/residue: 0.6198 time to fit residues: 223.8760 Evaluate side-chains 273 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 218 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 687 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 491 GLN Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 443 TYR Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 12 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 219 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 725 HIS A 818 GLN B 493 GLN B 538 ASN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 536 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 240 HIS D 370 ASN E 52 ASN E 391 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.152043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.117351 restraints weight = 26279.671| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.97 r_work: 0.2962 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22869 Z= 0.182 Angle : 0.606 7.865 31269 Z= 0.321 Chirality : 0.044 0.241 3547 Planarity : 0.004 0.048 3651 Dihedral : 18.190 170.643 3723 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.78 % Allowed : 14.58 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.16), residues: 2479 helix: -0.14 (0.14), residues: 1337 sheet: -0.81 (0.36), residues: 193 loop : -1.26 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 297 TYR 0.016 0.002 TYR E 38 PHE 0.023 0.002 PHE C 589 TRP 0.012 0.001 TRP C 494 HIS 0.007 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00436 (22869) covalent geometry : angle 0.60564 (31269) hydrogen bonds : bond 0.04338 ( 938) hydrogen bonds : angle 4.11935 ( 2639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 228 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8271 (mttm) cc_final: 0.7991 (mttm) REVERT: A 634 ASN cc_start: 0.8631 (m110) cc_final: 0.8357 (t0) REVERT: A 819 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: B 262 THR cc_start: 0.8346 (m) cc_final: 0.7940 (t) REVERT: B 270 THR cc_start: 0.7791 (m) cc_final: 0.7247 (p) REVERT: B 377 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8484 (mtmt) REVERT: B 555 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: B 568 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7041 (mp) REVERT: B 587 MET cc_start: 0.8577 (mtp) cc_final: 0.8299 (mtm) REVERT: C 201 MET cc_start: 0.9074 (mtm) cc_final: 0.8813 (mtm) REVERT: C 399 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7132 (mp0) REVERT: C 411 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6929 (tmm-80) REVERT: C 515 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8326 (mttt) REVERT: D 156 LYS cc_start: 0.8474 (mttt) cc_final: 0.7927 (mtpp) REVERT: D 242 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7564 (mtt90) REVERT: D 295 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7762 (mpt-90) REVERT: D 418 MET cc_start: 0.8373 (ttm) cc_final: 0.7917 (ttm) REVERT: D 465 GLN cc_start: 0.8513 (pt0) cc_final: 0.8251 (pt0) REVERT: D 499 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (t80) REVERT: E 1 MET cc_start: 0.6042 (mmm) cc_final: 0.5761 (mmm) REVERT: E 56 ASN cc_start: 0.8853 (p0) cc_final: 0.8648 (p0) REVERT: E 67 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7977 (mt) REVERT: E 86 LYS cc_start: 0.8433 (mttt) cc_final: 0.8104 (tppp) REVERT: E 95 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7458 (p) REVERT: E 103 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: E 170 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7543 (ptp) REVERT: E 245 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 274 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.3160 (p) REVERT: E 298 ASN cc_start: 0.7903 (m-40) cc_final: 0.6674 (p0) REVERT: E 344 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8033 (ttt90) REVERT: E 453 ASN cc_start: 0.8336 (p0) cc_final: 0.7973 (p0) REVERT: F 341 ARG cc_start: 0.6832 (ptt-90) cc_final: 0.6544 (ptp-110) REVERT: F 344 HIS cc_start: 0.7031 (t-90) cc_final: 0.6576 (m90) REVERT: F 354 MET cc_start: 0.7737 (mmp) cc_final: 0.7498 (mmm) REVERT: F 376 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: F 387 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7827 (t70) REVERT: F 388 ASP cc_start: 0.7983 (t0) cc_final: 0.7677 (t70) outliers start: 87 outliers final: 41 residues processed: 291 average time/residue: 0.6334 time to fit residues: 210.7363 Evaluate side-chains 273 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 219 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 443 TYR Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 415 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 818 GLN A 820 GLN B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN C 600 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 158 HIS E 277 ASN E 391 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115416 restraints weight = 26413.348| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.03 r_work: 0.2930 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22869 Z= 0.258 Angle : 0.669 11.132 31269 Z= 0.349 Chirality : 0.047 0.273 3547 Planarity : 0.004 0.051 3651 Dihedral : 18.340 178.941 3723 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.25 % Allowed : 14.89 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.16), residues: 2479 helix: -0.07 (0.14), residues: 1338 sheet: -0.82 (0.35), residues: 202 loop : -1.16 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 297 TYR 0.018 0.002 TYR E 38 PHE 0.022 0.002 PHE E 256 TRP 0.011 0.002 TRP C 494 HIS 0.009 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00630 (22869) covalent geometry : angle 0.66858 (31269) hydrogen bonds : bond 0.04598 ( 938) hydrogen bonds : angle 4.17813 ( 2639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 231 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 634 ASN cc_start: 0.8632 (m110) cc_final: 0.8380 (t0) REVERT: A 819 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: B 262 THR cc_start: 0.8437 (m) cc_final: 0.8097 (t) REVERT: B 270 THR cc_start: 0.7876 (m) cc_final: 0.7350 (p) REVERT: B 288 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7339 (mmt-90) REVERT: B 384 VAL cc_start: 0.8589 (t) cc_final: 0.8347 (m) REVERT: B 536 MET cc_start: 0.8487 (mtp) cc_final: 0.8226 (mtm) REVERT: B 555 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: B 568 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7098 (mp) REVERT: B 587 MET cc_start: 0.8705 (mtp) cc_final: 0.8434 (mtm) REVERT: C 201 MET cc_start: 0.9077 (mtm) cc_final: 0.8822 (mtm) REVERT: C 399 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7217 (mp0) REVERT: C 411 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7073 (tmm160) REVERT: C 515 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8366 (mttt) REVERT: D 118 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8494 (mt) REVERT: D 156 LYS cc_start: 0.8461 (mttt) cc_final: 0.7922 (mtpp) REVERT: D 295 ARG cc_start: 0.8057 (mmt90) cc_final: 0.7802 (mpt-90) REVERT: D 418 MET cc_start: 0.8427 (ttm) cc_final: 0.7904 (ttm) REVERT: D 499 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8557 (t80) REVERT: E 67 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8056 (mt) REVERT: E 103 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: E 170 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.7694 (ptp) REVERT: E 245 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8572 (tm-30) REVERT: E 274 THR cc_start: 0.3543 (OUTLIER) cc_final: 0.3104 (p) REVERT: E 344 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8063 (ttt90) REVERT: E 453 ASN cc_start: 0.8550 (p0) cc_final: 0.8100 (p0) REVERT: F 341 ARG cc_start: 0.6873 (ptt-90) cc_final: 0.6577 (ptp-110) REVERT: F 344 HIS cc_start: 0.7015 (t-90) cc_final: 0.6545 (m90) REVERT: F 376 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: F 387 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7795 (t70) REVERT: F 388 ASP cc_start: 0.8026 (t0) cc_final: 0.7757 (t70) outliers start: 98 outliers final: 52 residues processed: 306 average time/residue: 0.6027 time to fit residues: 212.8029 Evaluate side-chains 282 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 102 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 535 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 499 PHE Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 443 TYR Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 415 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN E 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118929 restraints weight = 26356.878| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.05 r_work: 0.2963 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22869 Z= 0.144 Angle : 0.572 9.012 31269 Z= 0.305 Chirality : 0.042 0.218 3547 Planarity : 0.003 0.049 3651 Dihedral : 18.119 178.633 3723 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.69 % Allowed : 16.19 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.17), residues: 2479 helix: 0.27 (0.14), residues: 1338 sheet: -0.67 (0.36), residues: 202 loop : -1.08 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 297 TYR 0.015 0.001 TYR E 285 PHE 0.026 0.001 PHE C 589 TRP 0.013 0.001 TRP C 494 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00336 (22869) covalent geometry : angle 0.57234 (31269) hydrogen bonds : bond 0.04068 ( 938) hydrogen bonds : angle 3.98368 ( 2639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 241 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 634 ASN cc_start: 0.8575 (m110) cc_final: 0.8276 (t0) REVERT: A 819 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: B 262 THR cc_start: 0.8379 (m) cc_final: 0.8002 (t) REVERT: B 270 THR cc_start: 0.7750 (m) cc_final: 0.7245 (p) REVERT: B 288 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7138 (mmt-90) REVERT: B 377 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8520 (mtmt) REVERT: B 384 VAL cc_start: 0.8498 (t) cc_final: 0.8261 (m) REVERT: B 536 MET cc_start: 0.8406 (mtp) cc_final: 0.8091 (mtm) REVERT: B 555 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 568 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7130 (mp) REVERT: B 587 MET cc_start: 0.8630 (mtp) cc_final: 0.8273 (mtm) REVERT: C 201 MET cc_start: 0.9091 (mtm) cc_final: 0.8823 (mtm) REVERT: C 300 GLU cc_start: 0.8342 (pt0) cc_final: 0.7910 (tp30) REVERT: C 399 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7207 (mp0) REVERT: C 408 PHE cc_start: 0.7510 (t80) cc_final: 0.6836 (t80) REVERT: C 411 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6949 (tmm-80) REVERT: C 515 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8331 (mttt) REVERT: D 156 LYS cc_start: 0.8409 (mttt) cc_final: 0.7884 (mtpp) REVERT: D 242 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7460 (mtt90) REVERT: D 295 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7822 (mpt-90) REVERT: D 418 MET cc_start: 0.8408 (ttm) cc_final: 0.7929 (ttm) REVERT: D 465 GLN cc_start: 0.8616 (pt0) cc_final: 0.8353 (pt0) REVERT: E 67 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7969 (mt) REVERT: E 86 LYS cc_start: 0.8412 (mttt) cc_final: 0.8113 (tppp) REVERT: E 103 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: E 170 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8561 (mtt) REVERT: E 245 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8570 (tm-30) REVERT: E 274 THR cc_start: 0.3425 (OUTLIER) cc_final: 0.2893 (p) REVERT: E 296 ASP cc_start: 0.7062 (m-30) cc_final: 0.6730 (p0) REVERT: E 298 ASN cc_start: 0.7879 (m-40) cc_final: 0.6739 (p0) REVERT: E 344 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8063 (ttt90) REVERT: E 453 ASN cc_start: 0.8252 (p0) cc_final: 0.8012 (p0) REVERT: F 341 ARG cc_start: 0.6768 (ptt-90) cc_final: 0.6483 (ptp-110) REVERT: F 344 HIS cc_start: 0.7000 (t-90) cc_final: 0.6560 (m90) REVERT: F 354 MET cc_start: 0.7681 (mmp) cc_final: 0.7429 (mmm) REVERT: F 376 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: F 387 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7839 (t70) REVERT: F 388 ASP cc_start: 0.7892 (t0) cc_final: 0.7591 (t70) REVERT: F 408 THR cc_start: 0.8685 (t) cc_final: 0.8414 (p) outliers start: 85 outliers final: 37 residues processed: 304 average time/residue: 0.6409 time to fit residues: 223.6641 Evaluate side-chains 270 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 415 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 14 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN A 787 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 421 ASN C 536 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN E 391 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118580 restraints weight = 26400.029| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.10 r_work: 0.2985 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22869 Z= 0.135 Angle : 0.559 7.993 31269 Z= 0.298 Chirality : 0.042 0.158 3547 Planarity : 0.003 0.049 3651 Dihedral : 17.991 175.585 3723 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.30 % Allowed : 16.54 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.17), residues: 2479 helix: 0.52 (0.14), residues: 1344 sheet: -0.59 (0.36), residues: 202 loop : -1.04 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 297 TYR 0.014 0.001 TYR F 306 PHE 0.026 0.001 PHE C 395 TRP 0.013 0.001 TRP C 494 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00314 (22869) covalent geometry : angle 0.55894 (31269) hydrogen bonds : bond 0.03929 ( 938) hydrogen bonds : angle 3.91264 ( 2639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 238 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 634 ASN cc_start: 0.8587 (m110) cc_final: 0.8251 (t0) REVERT: A 819 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: B 262 THR cc_start: 0.8540 (m) cc_final: 0.8126 (t) REVERT: B 270 THR cc_start: 0.7737 (m) cc_final: 0.7256 (p) REVERT: B 288 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7227 (mmt-90) REVERT: B 377 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8529 (mtmt) REVERT: B 384 VAL cc_start: 0.8533 (t) cc_final: 0.8288 (m) REVERT: B 387 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 536 MET cc_start: 0.8377 (mtp) cc_final: 0.8147 (mtm) REVERT: B 555 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: B 568 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 587 MET cc_start: 0.8650 (mtp) cc_final: 0.8376 (mtm) REVERT: C 194 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8460 (mt) REVERT: C 201 MET cc_start: 0.9090 (mtm) cc_final: 0.8830 (mtm) REVERT: C 300 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: C 399 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7155 (mp0) REVERT: C 411 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6886 (tmm-80) REVERT: C 515 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8324 (mttt) REVERT: D 156 LYS cc_start: 0.8343 (mttt) cc_final: 0.7844 (mtpp) REVERT: D 242 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7439 (mtt90) REVERT: D 295 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7764 (mpt-90) REVERT: D 418 MET cc_start: 0.8411 (ttm) cc_final: 0.7944 (ttm) REVERT: D 465 GLN cc_start: 0.8619 (pt0) cc_final: 0.8367 (pt0) REVERT: E 67 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7929 (mt) REVERT: E 86 LYS cc_start: 0.8417 (mttt) cc_final: 0.8119 (tppp) REVERT: E 103 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: E 170 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: E 245 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8587 (tm-30) REVERT: E 274 THR cc_start: 0.3369 (OUTLIER) cc_final: 0.2944 (p) REVERT: E 296 ASP cc_start: 0.7088 (m-30) cc_final: 0.6757 (p0) REVERT: E 298 ASN cc_start: 0.7892 (m-40) cc_final: 0.6763 (p0) REVERT: E 344 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8037 (ttt90) REVERT: E 453 ASN cc_start: 0.8263 (p0) cc_final: 0.7995 (p0) REVERT: F 341 ARG cc_start: 0.6829 (ptt-90) cc_final: 0.6560 (ptp-110) REVERT: F 354 MET cc_start: 0.7628 (mmp) cc_final: 0.7405 (mmm) REVERT: F 376 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: F 387 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7794 (t70) REVERT: F 388 ASP cc_start: 0.7799 (t0) cc_final: 0.7463 (t70) REVERT: F 408 THR cc_start: 0.8723 (t) cc_final: 0.8486 (p) outliers start: 76 outliers final: 37 residues processed: 290 average time/residue: 0.6346 time to fit residues: 210.3733 Evaluate side-chains 277 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 224 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN D 240 HIS E 391 GLN E 440 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.149551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115052 restraints weight = 26390.110| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.94 r_work: 0.2922 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 22869 Z= 0.273 Angle : 0.672 11.113 31269 Z= 0.350 Chirality : 0.047 0.198 3547 Planarity : 0.004 0.050 3651 Dihedral : 18.231 175.449 3723 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.60 % Allowed : 16.75 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.16), residues: 2479 helix: 0.30 (0.14), residues: 1339 sheet: -0.69 (0.35), residues: 202 loop : -1.06 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 297 TYR 0.017 0.002 TYR E 38 PHE 0.065 0.002 PHE E 264 TRP 0.012 0.002 TRP C 494 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00667 (22869) covalent geometry : angle 0.67247 (31269) hydrogen bonds : bond 0.04493 ( 938) hydrogen bonds : angle 4.11078 ( 2639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 222 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 502 GLN cc_start: 0.8041 (tt0) cc_final: 0.7620 (tt0) REVERT: A 819 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: B 262 THR cc_start: 0.8417 (m) cc_final: 0.8124 (t) REVERT: B 270 THR cc_start: 0.7784 (m) cc_final: 0.7286 (p) REVERT: B 288 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7151 (mmt-90) REVERT: B 384 VAL cc_start: 0.8507 (t) cc_final: 0.8290 (m) REVERT: B 387 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: B 536 MET cc_start: 0.8530 (mtp) cc_final: 0.8203 (mtm) REVERT: B 555 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: B 568 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7150 (mp) REVERT: B 572 GLU cc_start: 0.7675 (tp30) cc_final: 0.7343 (tm-30) REVERT: B 587 MET cc_start: 0.8731 (mtp) cc_final: 0.8418 (mtm) REVERT: C 147 MET cc_start: 0.9495 (mmp) cc_final: 0.9237 (mmp) REVERT: C 201 MET cc_start: 0.9084 (mtm) cc_final: 0.8814 (mtm) REVERT: C 300 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7955 (tp30) REVERT: C 399 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7262 (mp0) REVERT: C 408 PHE cc_start: 0.7614 (t80) cc_final: 0.7289 (t80) REVERT: C 411 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6965 (tmm160) REVERT: C 515 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8354 (mttt) REVERT: D 156 LYS cc_start: 0.8423 (mttt) cc_final: 0.7935 (mtpp) REVERT: D 295 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7759 (mpt-90) REVERT: D 418 MET cc_start: 0.8437 (ttm) cc_final: 0.7937 (ttm) REVERT: E 67 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8050 (mt) REVERT: E 103 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: E 170 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.7826 (ptp) REVERT: E 245 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8569 (tm-30) REVERT: E 274 THR cc_start: 0.3453 (OUTLIER) cc_final: 0.3013 (p) REVERT: E 296 ASP cc_start: 0.7055 (m-30) cc_final: 0.6803 (p0) REVERT: E 344 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8057 (ttt90) REVERT: E 453 ASN cc_start: 0.8500 (p0) cc_final: 0.8064 (p0) REVERT: F 341 ARG cc_start: 0.6830 (ptt-90) cc_final: 0.6579 (ptp-110) REVERT: F 376 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: F 387 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7879 (t70) REVERT: F 388 ASP cc_start: 0.7806 (t0) cc_final: 0.7505 (t70) REVERT: F 408 THR cc_start: 0.8683 (t) cc_final: 0.8440 (p) outliers start: 83 outliers final: 46 residues processed: 277 average time/residue: 0.6525 time to fit residues: 206.9332 Evaluate side-chains 270 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 211 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 288 ARG Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 415 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 230 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 536 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119667 restraints weight = 26480.328| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.12 r_work: 0.2984 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22869 Z= 0.129 Angle : 0.571 10.029 31269 Z= 0.302 Chirality : 0.042 0.154 3547 Planarity : 0.003 0.048 3651 Dihedral : 18.058 179.984 3723 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.65 % Allowed : 17.80 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2479 helix: 0.58 (0.14), residues: 1338 sheet: -0.68 (0.35), residues: 202 loop : -1.01 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 297 TYR 0.013 0.001 TYR F 306 PHE 0.026 0.001 PHE C 408 TRP 0.013 0.001 TRP C 494 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00301 (22869) covalent geometry : angle 0.57085 (31269) hydrogen bonds : bond 0.03952 ( 938) hydrogen bonds : angle 3.93502 ( 2639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4958 Ramachandran restraints generated. 2479 Oldfield, 0 Emsley, 2479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 407 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6374 (pt0) REVERT: A 819 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: A 879 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8823 (mp) REVERT: B 262 THR cc_start: 0.8572 (m) cc_final: 0.8159 (t) REVERT: B 270 THR cc_start: 0.7726 (m) cc_final: 0.7248 (p) REVERT: B 384 VAL cc_start: 0.8574 (t) cc_final: 0.8344 (m) REVERT: B 387 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: B 536 MET cc_start: 0.8514 (mtp) cc_final: 0.8227 (mtm) REVERT: B 568 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7154 (mp) REVERT: B 587 MET cc_start: 0.8656 (mtp) cc_final: 0.8286 (mtm) REVERT: C 147 MET cc_start: 0.9460 (mmp) cc_final: 0.9217 (mmp) REVERT: C 194 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (mt) REVERT: C 201 MET cc_start: 0.9096 (mtm) cc_final: 0.8824 (mtm) REVERT: C 300 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: C 399 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7251 (mp0) REVERT: C 408 PHE cc_start: 0.7624 (t80) cc_final: 0.7319 (t80) REVERT: C 411 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6820 (tmm-80) REVERT: C 515 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8343 (mttt) REVERT: D 156 LYS cc_start: 0.8345 (mttt) cc_final: 0.7867 (mtpp) REVERT: D 295 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7798 (mpt-90) REVERT: D 418 MET cc_start: 0.8433 (ttm) cc_final: 0.7974 (ttm) REVERT: E 103 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: E 170 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (mtt) REVERT: E 245 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8559 (tm-30) REVERT: E 274 THR cc_start: 0.3371 (OUTLIER) cc_final: 0.2933 (p) REVERT: E 290 LYS cc_start: 0.8163 (mttm) cc_final: 0.7109 (ptmt) REVERT: E 296 ASP cc_start: 0.7047 (m-30) cc_final: 0.6756 (p0) REVERT: E 298 ASN cc_start: 0.7881 (m-40) cc_final: 0.6749 (p0) REVERT: E 344 ARG cc_start: 0.8354 (ttp-110) cc_final: 0.8045 (ttt90) REVERT: E 453 ASN cc_start: 0.8233 (p0) cc_final: 0.7986 (p0) REVERT: F 341 ARG cc_start: 0.6856 (ptt-90) cc_final: 0.6559 (ptp-110) REVERT: F 354 MET cc_start: 0.7653 (mmp) cc_final: 0.7438 (mmm) REVERT: F 376 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: F 387 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7799 (t70) REVERT: F 388 ASP cc_start: 0.7743 (t0) cc_final: 0.7424 (t70) REVERT: F 408 THR cc_start: 0.8708 (t) cc_final: 0.8492 (p) outliers start: 61 outliers final: 38 residues processed: 271 average time/residue: 0.6245 time to fit residues: 194.1063 Evaluate side-chains 269 residues out of total 2304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 411 ARG Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 467 ASP Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 264 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 395 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 107 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 253 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN B 493 GLN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 536 ASN C 600 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.151268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.116941 restraints weight = 26456.370| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.14 r_work: 0.2931 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22869 Z= 0.215 Angle : 0.619 9.819 31269 Z= 0.323 Chirality : 0.045 0.168 3547 Planarity : 0.004 0.051 3651 Dihedral : 18.085 177.287 3723 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.73 % Allowed : 17.97 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.17), residues: 2479 helix: 0.49 (0.14), residues: 1339 sheet: -0.71 (0.35), residues: 202 loop : -1.00 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 297 TYR 0.020 0.002 TYR E 285 PHE 0.025 0.002 PHE C 408 TRP 0.013 0.001 TRP C 494 HIS 0.008 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00525 (22869) covalent geometry : angle 0.61896 (31269) hydrogen bonds : bond 0.04193 ( 938) hydrogen bonds : angle 3.99628 ( 2639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7684.62 seconds wall clock time: 131 minutes 42.22 seconds (7902.22 seconds total)