Starting phenix.real_space_refine on Mon Sep 14 08:47:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6j_21557/09_2026/6w6j_21557_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 70 5.16 5 C 18133 2.51 5 N 5326 2.21 5 O 5677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29240 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4796 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 24, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 5393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5393 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 34, 'TRANS': 672} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4702 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.71, per 1000 atoms: 0.23 Number of scatterers: 29240 At special positions: 0 Unit cell: (137.472, 146.064, 138.546, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 34 15.00 O 5677 8.00 N 5326 7.00 C 18133 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6902 Finding SS restraints... Secondary structure from input PDB file: 193 helices and 28 sheets defined 54.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.669A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.631A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.858A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.621A pdb=" N ARG A 233 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.729A pdb=" N SER A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 317 through 324 removed outlier: 4.274A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.691A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 5.647A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.604A pdb=" N LEU A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 391 through 407 removed outlier: 4.272A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.512A pdb=" N ARG A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 469 removed outlier: 3.586A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.932A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.811A pdb=" N LYS A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.955A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.539A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.711A pdb=" N ALA A 667 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 687 through 690 Processing helix chain 'A' and resid 691 through 696 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.919A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 757 through 760 Processing helix chain 'A' and resid 761 through 776 removed outlier: 3.914A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.943A pdb=" N GLY A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.776A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.517A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.991A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.577A pdb=" N VAL B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.602A pdb=" N SER B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.815A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 4.789A pdb=" N MET B 303 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.665A pdb=" N TYR B 320 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.716A pdb=" N PHE B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.531A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 377 removed outlier: 3.528A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.609A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 3.508A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 469 removed outlier: 4.475A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 448 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.746A pdb=" N LYS B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.937A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.989A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 626 removed outlier: 3.956A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 3.644A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 647 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.616A pdb=" N LYS B 683 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 693 Processing helix chain 'B' and resid 731 through 736 removed outlier: 3.704A pdb=" N ARG B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 777 removed outlier: 3.811A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.730A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 824 removed outlier: 3.552A pdb=" N ARG B 809 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.670A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.963A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.662A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 306 removed outlier: 3.932A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.715A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.561A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 381 removed outlier: 3.609A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.734A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.800A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 469 removed outlier: 4.386A pdb=" N GLU C 440 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 557 through 569 removed outlier: 5.668A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 591 removed outlier: 4.056A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 626 Processing helix chain 'C' and resid 627 through 631 removed outlier: 3.910A pdb=" N MET C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 3.517A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 647 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 680 through 684 removed outlier: 3.682A pdb=" N ALA C 684 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 730 through 739 removed outlier: 3.841A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 757 through 777 removed outlier: 3.864A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 786 through 796 removed outlier: 3.819A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 824 removed outlier: 5.269A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.910A pdb=" N LEU D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 53 removed outlier: 3.605A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 107 through 119 removed outlier: 3.527A pdb=" N ASP D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 removed outlier: 3.597A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.707A pdb=" N LYS D 163 " --> pdb=" O GLN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.542A pdb=" N GLU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.609A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.032A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 4.009A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 4.022A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.584A pdb=" N ILE D 283 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 343 through 362 removed outlier: 5.400A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 362 " --> pdb=" O TYR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 removed outlier: 3.687A pdb=" N LEU D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 407 removed outlier: 4.153A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 545 removed outlier: 3.792A pdb=" N ILE D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 539 " --> pdb=" O PRO D 535 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 removed outlier: 3.604A pdb=" N ARG D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.687A pdb=" N GLU D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.554A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 626 Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 642 through 648 removed outlier: 3.665A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.797A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 4.004A pdb=" N LEU D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 739 Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 757 through 760 Processing helix chain 'D' and resid 761 through 776 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 807 through 815 Processing helix chain 'D' and resid 815 through 821 Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 184 through 194 removed outlier: 3.878A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 241 through 245 removed outlier: 3.520A pdb=" N SER E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 316 through 324 Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.763A pdb=" N PHE E 334 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 354 removed outlier: 3.778A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 386 through 405 removed outlier: 3.935A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 547 removed outlier: 4.588A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 575 through 590 Processing helix chain 'E' and resid 612 through 625 removed outlier: 4.236A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 649 removed outlier: 3.841A pdb=" N VAL E 645 " --> pdb=" O LYS E 642 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 684 Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.937A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 739 removed outlier: 4.122A pdb=" N ALA E 733 " --> pdb=" O GLU E 729 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 739 " --> pdb=" O VAL E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 774 through 778 removed outlier: 4.031A pdb=" N GLN E 778 " --> pdb=" O ARG E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 793 Processing helix chain 'E' and resid 793 through 798 Processing helix chain 'E' and resid 808 through 820 removed outlier: 3.605A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 826 Processing helix chain 'F' and resid 169 through 175 removed outlier: 3.751A pdb=" N ARG F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 226 Processing helix chain 'F' and resid 257 through 269 removed outlier: 4.191A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.520A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 325 removed outlier: 3.909A pdb=" N GLU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 4.025A pdb=" N PHE F 334 " --> pdb=" O GLU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 359 removed outlier: 4.010A pdb=" N GLY F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 356 " --> pdb=" O ARG F 352 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 375 Processing helix chain 'F' and resid 377 through 382 removed outlier: 3.797A pdb=" N TYR F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 407 removed outlier: 4.957A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP F 407 " --> pdb=" O ARG F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 428 Processing helix chain 'F' and resid 438 through 469 removed outlier: 3.674A pdb=" N LYS F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 464 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 466 " --> pdb=" O ARG F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 544 removed outlier: 3.678A pdb=" N ALA F 539 " --> pdb=" O PRO F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 563 removed outlier: 4.002A pdb=" N LEU F 561 " --> pdb=" O GLU F 557 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 569 through 571 No H-bonds generated for 'chain 'F' and resid 569 through 571' Processing helix chain 'F' and resid 575 through 584 Processing helix chain 'F' and resid 586 through 591 Processing helix chain 'F' and resid 614 through 626 removed outlier: 3.636A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 625 " --> pdb=" O ALA F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 removed outlier: 3.651A pdb=" N MET F 631 " --> pdb=" O GLU F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.537A pdb=" N THR F 644 " --> pdb=" O GLU F 641 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 648 " --> pdb=" O VAL F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 669 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 688 through 699 removed outlier: 3.676A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASP F 697 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 698 " --> pdb=" O GLN F 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 739 Processing helix chain 'F' and resid 757 through 760 Processing helix chain 'F' and resid 761 through 776 Processing helix chain 'F' and resid 786 through 797 Processing helix chain 'F' and resid 804 through 824 removed outlier: 3.677A pdb=" N ARG F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 6.492A pdb=" N THR A 275 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA A 314 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 277 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N THR A 316 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 206 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 7.170A pdb=" N ARG A 365 " --> pdb=" O VAL A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 635 removed outlier: 8.657A pdb=" N LEU A 751 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET A 604 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 784 through 785 removed outlier: 6.801A pdb=" N GLN A 784 " --> pdb=" O VAL A 836 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.676A pdb=" N THR B 166 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N VAL B 312 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 275 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA B 314 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE B 277 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 315 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL B 203 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 635 removed outlier: 6.273A pdb=" N GLY B 601 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B 718 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE B 603 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AA9, first strand: chain 'B' and resid 782 through 785 removed outlier: 7.055A pdb=" N GLN B 782 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL B 836 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN B 784 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N VAL B 838 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 167 removed outlier: 6.646A pdb=" N THR C 275 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ALA C 314 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE C 277 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.410A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 602 through 603 removed outlier: 7.099A pdb=" N PHE C 603 " --> pdb=" O LEU C 718 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 700 through 702 removed outlier: 3.510A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.155A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AB7, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.207A pdb=" N VAL D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP D 278 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR D 275 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N ALA D 314 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE D 277 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N THR D 316 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 206 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.825A pdb=" N ARG D 365 " --> pdb=" O VAL D 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.159A pdb=" N VAL D 676 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR D 719 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE D 678 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 603 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER D 720 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE D 605 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 700 through 702 removed outlier: 3.548A pdb=" N LEU D 701 " --> pdb=" O VAL D 709 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 782 through 784 Processing sheet with id=AC3, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC4, first strand: chain 'E' and resid 237 through 240 Processing sheet with id=AC5, first strand: chain 'E' and resid 602 through 604 removed outlier: 7.722A pdb=" N PHE E 603 " --> pdb=" O LEU E 718 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 702 Processing sheet with id=AC7, first strand: chain 'F' and resid 276 through 278 removed outlier: 4.317A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU F 204 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL F 203 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 632 through 635 removed outlier: 6.857A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 719 " --> pdb=" O PHE F 678 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY F 601 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU F 718 " --> pdb=" O GLY F 601 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE F 603 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N SER F 720 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N PHE F 605 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N LEU F 751 " --> pdb=" O ALA F 602 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET F 604 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 700 through 702 Processing sheet with id=AD1, first strand: chain 'F' and resid 783 through 784 1166 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10418 1.36 - 1.51: 9067 1.51 - 1.66: 10020 1.66 - 1.80: 116 1.80 - 1.95: 14 Bond restraints: 29635 Sorted by residual: bond pdb=" O3B AGS B 902 " pdb=" PB AGS B 902 " ideal model delta sigma weight residual 1.673 1.559 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " ideal model delta sigma weight residual 1.673 1.559 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" O3B AGS A 902 " pdb=" PB AGS A 902 " ideal model delta sigma weight residual 1.673 1.563 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" O3A AGS C 902 " pdb=" PA AGS C 902 " ideal model delta sigma weight residual 1.664 1.554 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" O3A AGS A 901 " pdb=" PA AGS A 901 " ideal model delta sigma weight residual 1.664 1.555 0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 29630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 39456 3.01 - 6.02: 509 6.02 - 9.03: 85 9.03 - 12.04: 31 12.04 - 15.05: 14 Bond angle restraints: 40095 Sorted by residual: angle pdb=" N ILE F 413 " pdb=" CA ILE F 413 " pdb=" C ILE F 413 " ideal model delta sigma weight residual 113.53 105.07 8.46 9.80e-01 1.04e+00 7.44e+01 angle pdb=" N VAL E 801 " pdb=" CA VAL E 801 " pdb=" C VAL E 801 " ideal model delta sigma weight residual 113.53 106.18 7.35 9.80e-01 1.04e+00 5.62e+01 angle pdb=" N VAL B 801 " pdb=" CA VAL B 801 " pdb=" C VAL B 801 " ideal model delta sigma weight residual 113.71 107.37 6.34 9.50e-01 1.11e+00 4.45e+01 angle pdb=" N ILE C 413 " pdb=" CA ILE C 413 " pdb=" C ILE C 413 " ideal model delta sigma weight residual 112.12 106.89 5.23 8.40e-01 1.42e+00 3.87e+01 angle pdb=" N VAL C 246 " pdb=" CA VAL C 246 " pdb=" C VAL C 246 " ideal model delta sigma weight residual 111.91 107.37 4.54 8.90e-01 1.26e+00 2.61e+01 ... (remaining 40090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 17920 35.74 - 71.49: 448 71.49 - 107.23: 101 107.23 - 142.97: 10 142.97 - 178.72: 18 Dihedral angle restraints: 18497 sinusoidal: 7801 harmonic: 10696 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual 180.00 -117.78 -62.22 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA PHE C 386 " pdb=" C PHE C 386 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " ideal model delta harmonic sigma weight residual -180.00 -141.16 -38.84 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA PHE D 386 " pdb=" C PHE D 386 " pdb=" N LEU D 387 " pdb=" CA LEU D 387 " ideal model delta harmonic sigma weight residual 180.00 -144.55 -35.45 0 5.00e+00 4.00e-02 5.03e+01 ... (remaining 18494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3873 0.068 - 0.136: 641 0.136 - 0.203: 47 0.203 - 0.271: 5 0.271 - 0.339: 10 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C3' AGS A 901 " pdb=" C2' AGS A 901 " pdb=" C4' AGS A 901 " pdb=" O3' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.71 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C3' AGS C 902 " pdb=" C2' AGS C 902 " pdb=" C4' AGS C 902 " pdb=" O3' AGS C 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.68 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4573 not shown) Planarity restraints: 5253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 273 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ILE D 273 " 0.067 2.00e-02 2.50e+03 pdb=" O ILE D 273 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE D 274 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO B 388 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 812 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C GLN D 812 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN D 812 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 813 " 0.017 2.00e-02 2.50e+03 ... (remaining 5250 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 19 2.15 - 2.84: 10034 2.84 - 3.52: 38812 3.52 - 4.21: 63162 4.21 - 4.90: 111420 Nonbonded interactions: 223447 Sorted by model distance: nonbonded pdb=" NZ LYS D 250 " pdb=" N GLU E 254 " model vdw 1.459 2.560 nonbonded pdb=" OE2 GLU C 426 " pdb=" NH1 ARG D 352 " model vdw 1.709 3.120 nonbonded pdb=" OG1 THR E 614 " pdb=" O1A ADP E 902 " model vdw 1.813 3.040 nonbonded pdb=" CG2 ILE F 350 " pdb=" C2 ADP F 902 " model vdw 1.870 3.760 nonbonded pdb=" OG1 THR F 213 " pdb=" O1A ADP F 902 " model vdw 1.985 3.040 ... (remaining 223442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 901)) selection = (chain 'F' and (resid 159 through 407 or resid 530 through 901)) } 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: 4.010 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.009 0.732 29640 Z= 0.604 Angle : 0.993 15.055 40095 Z= 0.516 Chirality : 0.051 0.339 4576 Planarity : 0.005 0.095 5253 Dihedral : 18.517 178.718 11595 Min Nonbonded Distance : 1.459 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.48 % Rotamer: Outliers : 0.82 % Allowed : 9.55 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.11), residues: 3681 helix: -2.70 (0.09), residues: 1835 sheet: -2.99 (0.24), residues: 359 loop : -3.60 (0.13), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 333 TYR 0.019 0.002 TYR D 158 PHE 0.036 0.002 PHE B 798 TRP 0.025 0.002 TRP D 545 HIS 0.008 0.002 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.36 (29635) covalent geometry : angle 0.99302 / 0.52 (40095) hydrogen bonds : bond 0.18034 / 12.40 ( 1166) hydrogen bonds : angle 6.89421 / 4.84 ( 3309) Misc. bond : bond 0.37217 / 18.69 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 444 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 464 GLN cc_start: 0.7491 (mm110) cc_final: 0.7023 (mm-40) REVERT: B 462 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7163 (ttt180) REVERT: C 455 LYS cc_start: 0.7814 (tppt) cc_final: 0.7209 (ttpt) REVERT: C 458 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 462 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7407 (ttm-80) REVERT: D 133 PRO cc_start: 0.5849 (Cg_exo) cc_final: 0.5639 (Cg_endo) REVERT: D 331 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 404 MET cc_start: 0.8295 (mmm) cc_final: 0.8066 (tpt) REVERT: D 631 MET cc_start: 0.9068 (ptt) cc_final: 0.8825 (ptt) REVERT: E 163 LYS cc_start: 0.8659 (pttm) cc_final: 0.8262 (ptpp) REVERT: E 281 HIS cc_start: 0.6746 (p90) cc_final: 0.6322 (p90) REVERT: E 323 HIS cc_start: 0.7147 (m170) cc_final: 0.6670 (m170) REVERT: E 745 ASN cc_start: 0.9083 (m-40) cc_final: 0.8818 (m-40) REVERT: E 772 LEU cc_start: 0.8353 (pp) cc_final: 0.7945 (mt) REVERT: E 798 PHE cc_start: 0.5356 (t80) cc_final: 0.4769 (t80) REVERT: F 217 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7010 (mt-10) REVERT: F 299 MET cc_start: 0.5978 (ttt) cc_final: 0.4754 (ttt) REVERT: F 325 GLU cc_start: 0.7513 (tp30) cc_final: 0.6301 (tm-30) REVERT: F 385 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5753 (mmt90) REVERT: F 423 LEU cc_start: 0.8108 (mt) cc_final: 0.7657 (tt) REVERT: F 590 ARG cc_start: 0.6020 (mmt-90) cc_final: 0.5474 (tpt170) outliers start: 25 outliers final: 23 residues processed: 468 average time/residue: 0.2729 time to fit residues: 183.1936 Evaluate side-chains 236 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 833 THR Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 268 ASN A 323 HIS A 361 HIS A 705 HIS B 335 GLN B 361 HIS B 452 GLN B 643 HIS B 685 HIS C 272 GLN C 323 HIS C 335 GLN C 361 HIS C 663 GLN C 685 HIS D 11 GLN D 95 GLN D 129 HIS D 335 GLN D 643 HIS D 705 HIS E 201 ASN E 685 HIS F 685 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089846 restraints weight = 55712.046| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.79 r_work: 0.3039 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 29640 Z= 0.126 Angle : 0.657 14.072 40095 Z= 0.322 Chirality : 0.043 0.239 4576 Planarity : 0.005 0.080 5253 Dihedral : 15.686 178.800 4555 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.44 % Rotamer: Outliers : 1.32 % Allowed : 13.01 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.13), residues: 3681 helix: -1.07 (0.12), residues: 1814 sheet: -2.55 (0.24), residues: 393 loop : -2.74 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 233 TYR 0.010 0.001 TYR E 164 PHE 0.031 0.001 PHE F 386 TRP 0.020 0.001 TRP D 545 HIS 0.008 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (29635) covalent geometry : angle 0.65716 / 0.32 (40095) hydrogen bonds : bond 0.03427 / 2.31 ( 1166) hydrogen bonds : angle 4.81352 / 3.41 ( 3309) Misc. bond : bond 0.00360 / 0.24 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8799 (mmm) cc_final: 0.8570 (mmm) REVERT: A 322 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8529 (tttp) REVERT: A 631 MET cc_start: 0.8922 (ptt) cc_final: 0.8692 (ptp) REVERT: A 701 LEU cc_start: 0.8994 (pt) cc_final: 0.8617 (pt) REVERT: B 444 LYS cc_start: 0.8617 (tppt) cc_final: 0.8034 (mtmm) REVERT: B 462 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7306 (ttt180) REVERT: B 606 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9144 (pp) REVERT: C 422 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7687 (ttp-110) REVERT: C 455 LYS cc_start: 0.7479 (tppt) cc_final: 0.6895 (ttpt) REVERT: C 458 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 462 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7087 (ttm-80) REVERT: D 112 MET cc_start: 0.7721 (mmm) cc_final: 0.7369 (ttm) REVERT: D 250 LYS cc_start: 0.7746 (mttt) cc_final: 0.7350 (pptt) REVERT: D 331 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8596 (tm-30) REVERT: D 404 MET cc_start: 0.8687 (mmm) cc_final: 0.8391 (tpt) REVERT: D 631 MET cc_start: 0.9142 (ptt) cc_final: 0.8890 (ptt) REVERT: E 163 LYS cc_start: 0.8635 (pttm) cc_final: 0.8406 (ptpp) REVERT: E 217 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8279 (mt-10) REVERT: E 281 HIS cc_start: 0.7256 (p90) cc_final: 0.6538 (p90) REVERT: E 323 HIS cc_start: 0.7595 (m170) cc_final: 0.7203 (m170) REVERT: E 564 MET cc_start: 0.7777 (mmm) cc_final: 0.7517 (mmm) REVERT: E 745 ASN cc_start: 0.9174 (m-40) cc_final: 0.8927 (m-40) REVERT: E 772 LEU cc_start: 0.8534 (pp) cc_final: 0.8274 (mt) REVERT: E 778 GLN cc_start: 0.4724 (mp10) cc_final: 0.4519 (pm20) REVERT: E 798 PHE cc_start: 0.5665 (t80) cc_final: 0.4846 (t80) REVERT: F 217 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6911 (mt-10) REVERT: F 221 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6903 (tm-30) REVERT: F 245 MET cc_start: 0.4032 (OUTLIER) cc_final: 0.3261 (ttm) REVERT: F 273 ILE cc_start: 0.7113 (tt) cc_final: 0.6898 (mt) REVERT: F 325 GLU cc_start: 0.7710 (tp30) cc_final: 0.6444 (tm-30) REVERT: F 385 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5739 (mtt90) REVERT: F 423 LEU cc_start: 0.7361 (mt) cc_final: 0.6823 (tt) REVERT: F 590 ARG cc_start: 0.6601 (mmt-90) cc_final: 0.5594 (tpt90) REVERT: F 658 TYR cc_start: 0.7916 (t80) cc_final: 0.7582 (t80) outliers start: 40 outliers final: 19 residues processed: 291 average time/residue: 0.2298 time to fit residues: 101.9730 Evaluate side-chains 214 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 348 optimal weight: 7.9990 chunk 325 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN C 643 HIS D 837 ASN E 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.078204 restraints weight = 56078.090| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.40 r_work: 0.2881 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 29640 Z= 0.279 Angle : 0.763 13.387 40095 Z= 0.374 Chirality : 0.048 0.334 4576 Planarity : 0.006 0.103 5253 Dihedral : 15.004 176.844 4538 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.89 % Favored : 90.00 % Rotamer: Outliers : 2.77 % Allowed : 14.26 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3681 helix: -0.74 (0.12), residues: 1869 sheet: -2.37 (0.24), residues: 386 loop : -2.57 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 808 TYR 0.023 0.002 TYR A 251 PHE 0.037 0.003 PHE D 605 TRP 0.026 0.002 TRP D 545 HIS 0.010 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 (29635) covalent geometry : angle 0.76261 / 0.37 (40095) hydrogen bonds : bond 0.04925 / 3.29 ( 1166) hydrogen bonds : angle 4.83246 / 3.40 ( 3309) Misc. bond : bond 0.00160 / 0.10 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 193 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8786 (tttt) REVERT: A 428 MET cc_start: 0.8559 (ppp) cc_final: 0.8260 (ppp) REVERT: A 603 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7577 (p90) REVERT: A 781 LEU cc_start: 0.8767 (tp) cc_final: 0.8504 (tp) REVERT: B 265 ASP cc_start: 0.9041 (t70) cc_final: 0.8800 (t0) REVERT: B 444 LYS cc_start: 0.8774 (tppt) cc_final: 0.8054 (mtmm) REVERT: B 462 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7024 (ttt180) REVERT: B 606 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9298 (pp) REVERT: B 783 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8774 (pp) REVERT: C 280 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8980 (pp) REVERT: C 428 MET cc_start: 0.8552 (tmm) cc_final: 0.8329 (tmm) REVERT: C 455 LYS cc_start: 0.7637 (tppt) cc_final: 0.7002 (ttpt) REVERT: C 458 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 462 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.7113 (ttm-80) REVERT: D 112 MET cc_start: 0.7500 (mmm) cc_final: 0.7271 (ttt) REVERT: D 250 LYS cc_start: 0.8012 (mttt) cc_final: 0.7696 (pttp) REVERT: D 283 ILE cc_start: 0.9020 (tt) cc_final: 0.8816 (tt) REVERT: D 331 GLU cc_start: 0.9331 (tm-30) cc_final: 0.8998 (tm-30) REVERT: D 636 MET cc_start: 0.9355 (mmm) cc_final: 0.8675 (mmm) REVERT: D 685 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (p90) REVERT: D 827 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: E 164 TYR cc_start: 0.8148 (m-10) cc_final: 0.7698 (m-80) REVERT: E 319 GLU cc_start: 0.8232 (mm-30) cc_final: 0.6710 (mm-30) REVERT: E 323 HIS cc_start: 0.7740 (m170) cc_final: 0.6488 (m170) REVERT: E 365 ARG cc_start: 0.7082 (ttm110) cc_final: 0.6565 (ttp-110) REVERT: E 628 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7761 (pp20) REVERT: E 745 ASN cc_start: 0.9163 (m-40) cc_final: 0.8892 (m-40) REVERT: E 772 LEU cc_start: 0.8594 (pp) cc_final: 0.8240 (mt) REVERT: E 798 PHE cc_start: 0.5798 (t80) cc_final: 0.5019 (t80) REVERT: F 217 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7379 (mt-10) REVERT: F 245 MET cc_start: 0.4133 (OUTLIER) cc_final: 0.3675 (ttp) REVERT: F 273 ILE cc_start: 0.7521 (tt) cc_final: 0.7287 (mt) REVERT: F 325 GLU cc_start: 0.7735 (tp30) cc_final: 0.6552 (tm-30) REVERT: F 385 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5859 (mtt-85) REVERT: F 590 ARG cc_start: 0.6971 (mmt-90) cc_final: 0.5826 (tpt170) REVERT: F 629 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7690 (mtt180) REVERT: F 658 TYR cc_start: 0.7893 (t80) cc_final: 0.7549 (t80) REVERT: F 702 THR cc_start: 0.5455 (OUTLIER) cc_final: 0.5174 (p) REVERT: F 827 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7516 (pt0) outliers start: 84 outliers final: 43 residues processed: 266 average time/residue: 0.1973 time to fit residues: 82.5932 Evaluate side-chains 224 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 545 TRP Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 150 optimal weight: 0.7980 chunk 352 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 313 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.122141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.082623 restraints weight = 55567.012| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.77 r_work: 0.2932 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 29640 Z= 0.139 Angle : 0.624 12.643 40095 Z= 0.306 Chirality : 0.043 0.213 4576 Planarity : 0.005 0.093 5253 Dihedral : 14.352 174.923 4533 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.56 % Favored : 91.39 % Rotamer: Outliers : 2.01 % Allowed : 15.90 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.14), residues: 3681 helix: -0.30 (0.13), residues: 1858 sheet: -2.09 (0.24), residues: 372 loop : -2.36 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 421 TYR 0.014 0.001 TYR F 320 PHE 0.028 0.001 PHE D 798 TRP 0.021 0.001 TRP D 545 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (29635) covalent geometry : angle 0.62381 / 0.31 (40095) hydrogen bonds : bond 0.03505 / 2.36 ( 1166) hydrogen bonds : angle 4.47636 / 3.18 ( 3309) Misc. bond : bond 0.00198 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8055 (m-30) cc_final: 0.7778 (p0) REVERT: A 322 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8603 (tttm) REVERT: A 333 ARG cc_start: 0.8458 (mmt90) cc_final: 0.8145 (mmt90) REVERT: A 428 MET cc_start: 0.8385 (ppp) cc_final: 0.8105 (ppp) REVERT: A 603 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7352 (p90) REVERT: A 701 LEU cc_start: 0.9009 (pt) cc_final: 0.8585 (pt) REVERT: A 781 LEU cc_start: 0.8579 (tp) cc_final: 0.8022 (tp) REVERT: A 823 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9221 (tt) REVERT: B 265 ASP cc_start: 0.8873 (t70) cc_final: 0.8612 (t0) REVERT: B 444 LYS cc_start: 0.8704 (tppt) cc_final: 0.8008 (mtmm) REVERT: B 462 ARG cc_start: 0.7423 (ttp80) cc_final: 0.7136 (ttt180) REVERT: B 603 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8582 (p90) REVERT: B 606 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9237 (pp) REVERT: C 428 MET cc_start: 0.8404 (tmm) cc_final: 0.8160 (tmm) REVERT: C 455 LYS cc_start: 0.7621 (tppt) cc_final: 0.7034 (ttpt) REVERT: C 458 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7396 (tm-30) REVERT: C 462 ARG cc_start: 0.7429 (ttp-170) cc_final: 0.7093 (ttm-80) REVERT: D 250 LYS cc_start: 0.7769 (mttt) cc_final: 0.7556 (pptt) REVERT: D 331 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 404 MET cc_start: 0.8791 (mmm) cc_final: 0.8433 (tpt) REVERT: D 636 MET cc_start: 0.9155 (mmm) cc_final: 0.8623 (mmm) REVERT: E 164 TYR cc_start: 0.8059 (m-10) cc_final: 0.7728 (m-80) REVERT: E 319 GLU cc_start: 0.8153 (mm-30) cc_final: 0.6882 (mm-30) REVERT: E 323 HIS cc_start: 0.7797 (m170) cc_final: 0.6661 (m170) REVERT: E 365 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6683 (ttp-110) REVERT: E 564 MET cc_start: 0.7700 (mmm) cc_final: 0.7363 (mmm) REVERT: E 745 ASN cc_start: 0.9176 (m-40) cc_final: 0.8893 (m-40) REVERT: E 772 LEU cc_start: 0.8517 (pp) cc_final: 0.8206 (mt) REVERT: E 798 PHE cc_start: 0.6011 (t80) cc_final: 0.5188 (t80) REVERT: E 827 GLN cc_start: 0.4685 (tm-30) cc_final: 0.4449 (tt0) REVERT: F 217 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7385 (mt-10) REVERT: F 273 ILE cc_start: 0.7605 (tt) cc_final: 0.7393 (mt) REVERT: F 310 ARG cc_start: 0.6441 (mmp80) cc_final: 0.6219 (mmp80) REVERT: F 325 GLU cc_start: 0.7755 (tp30) cc_final: 0.6541 (tm-30) REVERT: F 385 ARG cc_start: 0.6143 (mtt180) cc_final: 0.5832 (mtt-85) REVERT: F 590 ARG cc_start: 0.6982 (mmt-90) cc_final: 0.5918 (tpt170) outliers start: 61 outliers final: 29 residues processed: 246 average time/residue: 0.1964 time to fit residues: 76.1366 Evaluate side-chains 209 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 25 optimal weight: 0.2980 chunk 92 optimal weight: 0.0770 chunk 141 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 281 HIS F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089357 restraints weight = 55555.111| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.59 r_work: 0.3023 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 29640 Z= 0.097 Angle : 0.571 12.170 40095 Z= 0.278 Chirality : 0.041 0.230 4576 Planarity : 0.004 0.084 5253 Dihedral : 13.824 167.952 4533 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.44 % Rotamer: Outliers : 1.75 % Allowed : 16.17 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3681 helix: 0.08 (0.13), residues: 1846 sheet: -2.03 (0.24), residues: 397 loop : -2.11 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 409 TYR 0.010 0.001 TYR D 158 PHE 0.028 0.001 PHE D 798 TRP 0.020 0.001 TRP D 545 HIS 0.004 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (29635) covalent geometry : angle 0.57091 / 0.28 (40095) hydrogen bonds : bond 0.02727 / 1.84 ( 1166) hydrogen bonds : angle 4.17188 / 2.97 ( 3309) Misc. bond : bond 0.00207 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7959 (m-30) cc_final: 0.7729 (p0) REVERT: A 322 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8679 (tttm) REVERT: A 333 ARG cc_start: 0.8419 (mmt90) cc_final: 0.8141 (mmt90) REVERT: A 428 MET cc_start: 0.8133 (ppp) cc_final: 0.7798 (ppp) REVERT: A 603 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7439 (p90) REVERT: A 701 LEU cc_start: 0.8922 (pt) cc_final: 0.8576 (pt) REVERT: B 265 ASP cc_start: 0.8777 (t70) cc_final: 0.8549 (t0) REVERT: B 444 LYS cc_start: 0.8597 (tppt) cc_final: 0.7934 (mtmm) REVERT: B 462 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6887 (ttt180) REVERT: B 603 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8265 (p90) REVERT: B 606 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 428 MET cc_start: 0.8295 (tmm) cc_final: 0.8029 (tmm) REVERT: C 455 LYS cc_start: 0.7599 (tppt) cc_final: 0.7043 (ttpt) REVERT: C 458 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 462 ARG cc_start: 0.7241 (ttp-170) cc_final: 0.6922 (ttm170) REVERT: C 827 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: D 250 LYS cc_start: 0.7769 (mttt) cc_final: 0.7360 (pptt) REVERT: D 331 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8735 (tm-30) REVERT: D 827 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: E 319 GLU cc_start: 0.8115 (mm-30) cc_final: 0.6926 (mm-30) REVERT: E 323 HIS cc_start: 0.7794 (m170) cc_final: 0.6656 (m170) REVERT: E 365 ARG cc_start: 0.6883 (ttm110) cc_final: 0.6505 (ttp-110) REVERT: E 564 MET cc_start: 0.7611 (mmm) cc_final: 0.7218 (mmm) REVERT: E 772 LEU cc_start: 0.8562 (pp) cc_final: 0.8341 (mt) REVERT: E 798 PHE cc_start: 0.5898 (t80) cc_final: 0.5051 (t80) REVERT: E 827 GLN cc_start: 0.4886 (tm-30) cc_final: 0.4669 (tt0) REVERT: F 217 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7332 (mt-10) REVERT: F 245 MET cc_start: 0.4035 (ttp) cc_final: 0.3656 (mtt) REVERT: F 273 ILE cc_start: 0.7658 (tt) cc_final: 0.7449 (mt) REVERT: F 310 ARG cc_start: 0.6471 (mmp80) cc_final: 0.6163 (mmp80) REVERT: F 325 GLU cc_start: 0.7689 (tp30) cc_final: 0.6485 (tm-30) REVERT: F 385 ARG cc_start: 0.6005 (mtt180) cc_final: 0.5796 (mtt-85) REVERT: F 590 ARG cc_start: 0.6908 (mmt-90) cc_final: 0.6075 (tpt90) REVERT: F 622 ASP cc_start: 0.7753 (t70) cc_final: 0.7482 (t0) outliers start: 53 outliers final: 24 residues processed: 253 average time/residue: 0.1956 time to fit residues: 79.0534 Evaluate side-chains 210 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 566 ASP Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 69 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 350 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN F 452 GLN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081042 restraints weight = 55078.491| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.37 r_work: 0.2948 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29640 Z= 0.147 Angle : 0.622 12.096 40095 Z= 0.301 Chirality : 0.043 0.281 4576 Planarity : 0.005 0.096 5253 Dihedral : 13.964 168.570 4533 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.75 % Favored : 91.20 % Rotamer: Outliers : 2.04 % Allowed : 16.73 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.14), residues: 3681 helix: 0.20 (0.13), residues: 1861 sheet: -1.88 (0.24), residues: 384 loop : -2.06 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 409 TYR 0.013 0.001 TYR F 320 PHE 0.034 0.002 PHE D 798 TRP 0.019 0.001 TRP D 545 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (29635) covalent geometry : angle 0.62191 / 0.30 (40095) hydrogen bonds : bond 0.03473 / 2.32 ( 1166) hydrogen bonds : angle 4.20035 / 2.98 ( 3309) Misc. bond : bond 0.00216 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8821 (tttt) REVERT: A 333 ARG cc_start: 0.8599 (mmt90) cc_final: 0.8337 (mmt90) REVERT: A 412 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8121 (pm20) REVERT: A 428 MET cc_start: 0.8347 (ppp) cc_final: 0.7912 (ppp) REVERT: A 603 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7646 (p90) REVERT: A 700 ARG cc_start: 0.8988 (ptt-90) cc_final: 0.8734 (ppt170) REVERT: A 701 LEU cc_start: 0.9000 (pt) cc_final: 0.8616 (pt) REVERT: B 265 ASP cc_start: 0.9066 (t70) cc_final: 0.8760 (t0) REVERT: B 428 MET cc_start: 0.8692 (tmm) cc_final: 0.8426 (tpp) REVERT: B 444 LYS cc_start: 0.8635 (tppt) cc_final: 0.7965 (mtmm) REVERT: B 462 ARG cc_start: 0.7284 (ttp80) cc_final: 0.6899 (ttt180) REVERT: B 603 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8576 (p90) REVERT: B 606 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9307 (pp) REVERT: C 428 MET cc_start: 0.8465 (tmm) cc_final: 0.8154 (tmm) REVERT: C 455 LYS cc_start: 0.7619 (tppt) cc_final: 0.7032 (ttpt) REVERT: C 458 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7470 (tm-30) REVERT: C 462 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6997 (ttm170) REVERT: C 827 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: D 250 LYS cc_start: 0.7951 (mttt) cc_final: 0.7605 (pptt) REVERT: D 331 GLU cc_start: 0.9364 (tm-30) cc_final: 0.9028 (tm-30) REVERT: D 827 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: E 254 GLU cc_start: 0.6985 (mm-30) cc_final: 0.5746 (mm-30) REVERT: E 323 HIS cc_start: 0.7690 (m170) cc_final: 0.7453 (m170) REVERT: E 365 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6673 (ttp-110) REVERT: E 564 MET cc_start: 0.7805 (mmm) cc_final: 0.7358 (mmm) REVERT: E 745 ASN cc_start: 0.9189 (m-40) cc_final: 0.8916 (m-40) REVERT: E 772 LEU cc_start: 0.8499 (pp) cc_final: 0.8187 (tp) REVERT: E 798 PHE cc_start: 0.6036 (t80) cc_final: 0.5103 (t80) REVERT: E 822 MET cc_start: 0.4438 (tpt) cc_final: 0.3973 (tpt) REVERT: E 827 GLN cc_start: 0.5188 (tm-30) cc_final: 0.4688 (tt0) REVERT: F 217 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7419 (mt-10) REVERT: F 221 GLN cc_start: 0.7856 (tp-100) cc_final: 0.6867 (mt0) REVERT: F 245 MET cc_start: 0.4527 (ttp) cc_final: 0.3817 (mtt) REVERT: F 273 ILE cc_start: 0.7777 (tt) cc_final: 0.7551 (mt) REVERT: F 310 ARG cc_start: 0.6664 (mmp80) cc_final: 0.6303 (mmp80) REVERT: F 325 GLU cc_start: 0.7754 (tp30) cc_final: 0.6395 (tm-30) REVERT: F 590 ARG cc_start: 0.7009 (mmt-90) cc_final: 0.6032 (tpt90) outliers start: 62 outliers final: 42 residues processed: 241 average time/residue: 0.1937 time to fit residues: 74.1912 Evaluate side-chains 216 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 545 TRP Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 304 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 312 optimal weight: 0.8980 chunk 325 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.123063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082533 restraints weight = 55396.767| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.39 r_work: 0.2979 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29640 Z= 0.110 Angle : 0.588 11.830 40095 Z= 0.284 Chirality : 0.042 0.263 4576 Planarity : 0.004 0.090 5253 Dihedral : 13.834 168.666 4533 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.53 % Favored : 91.42 % Rotamer: Outliers : 1.98 % Allowed : 16.99 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.14), residues: 3681 helix: 0.36 (0.13), residues: 1856 sheet: -1.80 (0.25), residues: 383 loop : -1.97 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 700 TYR 0.010 0.001 TYR B 655 PHE 0.032 0.001 PHE D 798 TRP 0.018 0.001 TRP D 545 HIS 0.007 0.001 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (29635) covalent geometry : angle 0.58794 / 0.28 (40095) hydrogen bonds : bond 0.02973 / 1.99 ( 1166) hydrogen bonds : angle 4.08633 / 2.90 ( 3309) Misc. bond : bond 0.00221 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8171 (m-30) cc_final: 0.7809 (p0) REVERT: A 333 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8341 (mmt90) REVERT: A 412 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 428 MET cc_start: 0.8267 (ppp) cc_final: 0.7854 (ppp) REVERT: A 459 LEU cc_start: 0.7138 (tp) cc_final: 0.6719 (mt) REVERT: A 603 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A 700 ARG cc_start: 0.8980 (ptt-90) cc_final: 0.8760 (ppt170) REVERT: A 701 LEU cc_start: 0.8963 (pt) cc_final: 0.8569 (pt) REVERT: B 265 ASP cc_start: 0.9062 (t70) cc_final: 0.8718 (m-30) REVERT: B 428 MET cc_start: 0.8695 (tmm) cc_final: 0.8407 (tpp) REVERT: B 444 LYS cc_start: 0.8532 (tppt) cc_final: 0.7854 (mtmm) REVERT: B 462 ARG cc_start: 0.7101 (ttp80) cc_final: 0.6703 (ttt180) REVERT: B 603 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8472 (p90) REVERT: B 606 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9281 (pp) REVERT: C 428 MET cc_start: 0.8461 (tmm) cc_final: 0.8144 (tmm) REVERT: C 455 LYS cc_start: 0.7624 (tppt) cc_final: 0.7057 (ttpt) REVERT: C 458 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 462 ARG cc_start: 0.7398 (ttp-170) cc_final: 0.7016 (ttm170) REVERT: C 827 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: D 250 LYS cc_start: 0.7956 (mttt) cc_final: 0.7602 (pptt) REVERT: D 331 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9008 (tm-30) REVERT: D 827 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: E 217 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8383 (tp30) REVERT: E 254 GLU cc_start: 0.6830 (mm-30) cc_final: 0.5747 (mm-30) REVERT: E 319 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8157 (tp30) REVERT: E 365 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6618 (ttp-110) REVERT: E 564 MET cc_start: 0.7781 (mmm) cc_final: 0.7278 (mmm) REVERT: E 772 LEU cc_start: 0.8449 (pp) cc_final: 0.8195 (tp) REVERT: E 798 PHE cc_start: 0.6038 (t80) cc_final: 0.5176 (t80) REVERT: E 822 MET cc_start: 0.4391 (tpt) cc_final: 0.3900 (tpt) REVERT: E 827 GLN cc_start: 0.5253 (tm-30) cc_final: 0.4740 (tt0) REVERT: F 217 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7494 (mt-10) REVERT: F 245 MET cc_start: 0.4763 (ttp) cc_final: 0.3985 (mtt) REVERT: F 273 ILE cc_start: 0.7777 (tt) cc_final: 0.7543 (mt) REVERT: F 310 ARG cc_start: 0.6621 (mmp80) cc_final: 0.6230 (mmp80) REVERT: F 325 GLU cc_start: 0.7767 (tp30) cc_final: 0.6383 (tm-30) REVERT: F 590 ARG cc_start: 0.6912 (mmt-90) cc_final: 0.6002 (tpt90) outliers start: 60 outliers final: 43 residues processed: 232 average time/residue: 0.2024 time to fit residues: 74.5880 Evaluate side-chains 221 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 545 TRP Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 216 optimal weight: 0.9980 chunk 259 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 286 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 369 optimal weight: 0.0170 chunk 82 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 201 ASN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085352 restraints weight = 55384.531| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.63 r_work: 0.3004 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 29640 Z= 0.096 Angle : 0.569 14.732 40095 Z= 0.273 Chirality : 0.041 0.242 4576 Planarity : 0.004 0.087 5253 Dihedral : 13.675 168.374 4533 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.23 % Favored : 91.71 % Rotamer: Outliers : 1.61 % Allowed : 17.39 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3681 helix: 0.57 (0.13), residues: 1849 sheet: -1.66 (0.25), residues: 385 loop : -1.85 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 700 TYR 0.016 0.001 TYR F 320 PHE 0.030 0.001 PHE D 798 TRP 0.019 0.001 TRP D 545 HIS 0.007 0.001 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (29635) covalent geometry : angle 0.56915 / 0.27 (40095) hydrogen bonds : bond 0.02630 / 1.76 ( 1166) hydrogen bonds : angle 3.96337 / 2.82 ( 3309) Misc. bond : bond 0.00215 / 0.15 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.7951 (m-30) cc_final: 0.7711 (p0) REVERT: A 333 ARG cc_start: 0.8456 (mmt90) cc_final: 0.8162 (mmt90) REVERT: A 428 MET cc_start: 0.8094 (ppp) cc_final: 0.7691 (ppp) REVERT: A 459 LEU cc_start: 0.7279 (tp) cc_final: 0.6852 (mt) REVERT: A 603 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7489 (p90) REVERT: A 701 LEU cc_start: 0.8878 (pt) cc_final: 0.8544 (pt) REVERT: B 265 ASP cc_start: 0.8845 (t70) cc_final: 0.8586 (m-30) REVERT: B 428 MET cc_start: 0.8653 (tmm) cc_final: 0.8341 (tpp) REVERT: B 444 LYS cc_start: 0.8555 (tppt) cc_final: 0.7912 (mtmm) REVERT: B 603 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8324 (p90) REVERT: B 606 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9147 (pp) REVERT: C 428 MET cc_start: 0.8338 (tmm) cc_final: 0.7998 (tmm) REVERT: C 455 LYS cc_start: 0.7722 (tppt) cc_final: 0.7178 (ttpt) REVERT: C 458 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 462 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.6998 (ttm170) REVERT: C 827 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: D 250 LYS cc_start: 0.7773 (mttt) cc_final: 0.7380 (pptt) REVERT: D 331 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8796 (tm-30) REVERT: D 404 MET cc_start: 0.8627 (mmm) cc_final: 0.8232 (tpt) REVERT: D 636 MET cc_start: 0.9054 (mmm) cc_final: 0.8621 (mmm) REVERT: E 164 TYR cc_start: 0.8006 (m-80) cc_final: 0.7435 (m-80) REVERT: E 217 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8072 (tp30) REVERT: E 254 GLU cc_start: 0.6644 (mm-30) cc_final: 0.5679 (mm-30) REVERT: E 365 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6530 (ttp-110) REVERT: E 564 MET cc_start: 0.7614 (mmm) cc_final: 0.6996 (mmm) REVERT: E 745 ASN cc_start: 0.9207 (m-40) cc_final: 0.8954 (m-40) REVERT: E 798 PHE cc_start: 0.6124 (t80) cc_final: 0.5176 (t80) REVERT: E 827 GLN cc_start: 0.5676 (tm-30) cc_final: 0.5456 (tt0) REVERT: F 217 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7287 (mt-10) REVERT: F 221 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7034 (mt0) REVERT: F 245 MET cc_start: 0.4814 (ttp) cc_final: 0.3927 (mtt) REVERT: F 273 ILE cc_start: 0.7784 (tt) cc_final: 0.7572 (mt) REVERT: F 325 GLU cc_start: 0.7654 (tp30) cc_final: 0.6257 (tm-30) REVERT: F 564 MET cc_start: 0.7447 (tpt) cc_final: 0.7205 (tpt) REVERT: F 590 ARG cc_start: 0.6962 (mmt-90) cc_final: 0.6014 (tpt90) outliers start: 49 outliers final: 36 residues processed: 242 average time/residue: 0.1957 time to fit residues: 75.3331 Evaluate side-chains 213 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 545 TRP Chi-restraints excluded: chain E residue 595 ASP Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 824 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 264 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 325 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.122176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081700 restraints weight = 56095.602| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.50 r_work: 0.3009 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29640 Z= 0.202 Angle : 0.670 13.798 40095 Z= 0.324 Chirality : 0.045 0.261 4576 Planarity : 0.005 0.101 5253 Dihedral : 13.979 169.542 4531 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.18 % Favored : 90.74 % Rotamer: Outliers : 2.01 % Allowed : 17.52 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3681 helix: 0.46 (0.13), residues: 1868 sheet: -1.77 (0.25), residues: 392 loop : -1.89 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 671 TYR 0.015 0.002 TYR A 251 PHE 0.030 0.002 PHE D 798 TRP 0.017 0.001 TRP D 545 HIS 0.005 0.001 HIS A 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.20 (29635) covalent geometry : angle 0.67024 / 0.32 (40095) hydrogen bonds : bond 0.03934 / 2.63 ( 1166) hydrogen bonds : angle 4.21489 / 2.98 ( 3309) Misc. bond : bond 0.00210 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8314 (mmt90) REVERT: A 428 MET cc_start: 0.8311 (ppp) cc_final: 0.7993 (ppp) REVERT: A 603 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7691 (p90) REVERT: B 265 ASP cc_start: 0.9042 (t70) cc_final: 0.8731 (m-30) REVERT: B 424 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 428 MET cc_start: 0.8675 (tmm) cc_final: 0.8376 (tpp) REVERT: B 444 LYS cc_start: 0.8597 (tppt) cc_final: 0.7915 (mtmm) REVERT: B 603 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8610 (p90) REVERT: B 606 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9320 (pp) REVERT: C 428 MET cc_start: 0.8502 (tmm) cc_final: 0.8157 (tmm) REVERT: C 455 LYS cc_start: 0.7610 (tppt) cc_final: 0.7033 (ttpt) REVERT: C 462 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.7015 (ttm170) REVERT: C 827 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: D 112 MET cc_start: 0.7388 (mmm) cc_final: 0.7008 (mtt) REVERT: D 250 LYS cc_start: 0.8034 (mttt) cc_final: 0.7653 (pttp) REVERT: D 331 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8960 (tm-30) REVERT: D 827 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: E 164 TYR cc_start: 0.8227 (m-80) cc_final: 0.7655 (m-80) REVERT: E 254 GLU cc_start: 0.6912 (mm-30) cc_final: 0.5506 (mm-30) REVERT: E 323 HIS cc_start: 0.7742 (m170) cc_final: 0.7355 (m-70) REVERT: E 365 ARG cc_start: 0.7203 (ttm110) cc_final: 0.6738 (ttp-110) REVERT: E 798 PHE cc_start: 0.6434 (t80) cc_final: 0.5659 (t80) REVERT: F 217 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7530 (mt-10) REVERT: F 221 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7123 (mt0) REVERT: F 325 GLU cc_start: 0.7852 (tp30) cc_final: 0.6420 (tm-30) REVERT: F 590 ARG cc_start: 0.6972 (mmt-90) cc_final: 0.6074 (tpt-90) outliers start: 61 outliers final: 46 residues processed: 229 average time/residue: 0.2002 time to fit residues: 73.0159 Evaluate side-chains 217 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain B residue 839 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 545 TRP Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 214 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 chunk 317 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 268 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 237 optimal weight: 0.0670 chunk 230 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 41 GLN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.125337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.085320 restraints weight = 55793.839| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.51 r_work: 0.3074 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 29640 Z= 0.105 Angle : 0.595 14.960 40095 Z= 0.287 Chirality : 0.041 0.245 4576 Planarity : 0.004 0.090 5253 Dihedral : 13.761 169.565 4531 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.55 % Rotamer: Outliers : 1.28 % Allowed : 18.37 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3681 helix: 0.67 (0.13), residues: 1858 sheet: -1.63 (0.25), residues: 388 loop : -1.84 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 310 TYR 0.016 0.001 TYR F 320 PHE 0.017 0.001 PHE F 386 TRP 0.019 0.001 TRP D 545 HIS 0.007 0.001 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (29635) covalent geometry : angle 0.59501 / 0.29 (40095) hydrogen bonds : bond 0.02864 / 1.93 ( 1166) hydrogen bonds : angle 4.03525 / 2.87 ( 3309) Misc. bond : bond 0.00212 / 0.15 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7362 Ramachandran restraints generated. 3681 Oldfield, 0 Emsley, 3681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8088 (m-30) cc_final: 0.7804 (p0) REVERT: A 333 ARG cc_start: 0.8531 (mmt90) cc_final: 0.8197 (mmt90) REVERT: A 428 MET cc_start: 0.8106 (ppp) cc_final: 0.7796 (ppp) REVERT: A 603 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7560 (p90) REVERT: A 701 LEU cc_start: 0.8887 (pt) cc_final: 0.8490 (pt) REVERT: B 265 ASP cc_start: 0.8773 (t70) cc_final: 0.8518 (m-30) REVERT: B 424 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7606 (mm-30) REVERT: B 444 LYS cc_start: 0.8529 (tppt) cc_final: 0.7894 (mtmm) REVERT: B 603 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8397 (p90) REVERT: B 606 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9192 (pp) REVERT: C 428 MET cc_start: 0.8414 (tmm) cc_final: 0.8061 (tmm) REVERT: C 455 LYS cc_start: 0.7519 (tppt) cc_final: 0.6963 (ttpt) REVERT: C 458 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7454 (tm-30) REVERT: C 462 ARG cc_start: 0.7229 (ttp-170) cc_final: 0.6891 (ttm170) REVERT: C 827 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: D 250 LYS cc_start: 0.7854 (mttt) cc_final: 0.7363 (pptt) REVERT: D 331 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8704 (tm-30) REVERT: D 404 MET cc_start: 0.8742 (mmm) cc_final: 0.8322 (tpt) REVERT: D 827 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: E 164 TYR cc_start: 0.8137 (m-80) cc_final: 0.7552 (m-80) REVERT: E 254 GLU cc_start: 0.6563 (mm-30) cc_final: 0.5249 (mm-30) REVERT: E 323 HIS cc_start: 0.7791 (m170) cc_final: 0.7465 (m-70) REVERT: E 365 ARG cc_start: 0.6985 (ttm110) cc_final: 0.6602 (ttp-110) REVERT: E 798 PHE cc_start: 0.6448 (t80) cc_final: 0.5522 (t80) REVERT: E 837 ASN cc_start: 0.8672 (m-40) cc_final: 0.7971 (p0) REVERT: F 217 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7462 (mt-10) REVERT: F 221 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7016 (mt0) REVERT: F 273 ILE cc_start: 0.7901 (tt) cc_final: 0.7675 (mt) REVERT: F 325 GLU cc_start: 0.7840 (tp30) cc_final: 0.6439 (tm-30) REVERT: F 590 ARG cc_start: 0.6890 (mmt-90) cc_final: 0.6117 (tpt-90) outliers start: 39 outliers final: 34 residues processed: 214 average time/residue: 0.1989 time to fit residues: 68.1079 Evaluate side-chains 203 residues out of total 3038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 697 ASP Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 742 GLU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 663 GLN Chi-restraints excluded: chain E residue 818 GLN Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 664 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 709 VAL Chi-restraints excluded: chain F residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 155 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 222 optimal weight: 0.4980 chunk 171 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 310 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085060 restraints weight = 56262.140| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.53 r_work: 0.3076 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 29640 Z= 0.108 Angle : 0.598 14.941 40095 Z= 0.286 Chirality : 0.042 0.245 4576 Planarity : 0.004 0.091 5253 Dihedral : 13.713 168.965 4531 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.66 % Rotamer: Outliers : 1.55 % Allowed : 18.21 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3681 helix: 0.76 (0.13), residues: 1862 sheet: -1.58 (0.25), residues: 395 loop : -1.83 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 763 TYR 0.009 0.001 TYR B 655 PHE 0.030 0.001 PHE D 798 TRP 0.018 0.001 TRP D 545 HIS 0.007 0.001 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (29635) covalent geometry : angle 0.59799 / 0.29 (40095) hydrogen bonds : bond 0.02895 / 1.94 ( 1166) hydrogen bonds : angle 3.99289 / 2.84 ( 3309) Misc. bond : bond 0.00202 / 0.14 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7160.76 seconds wall clock time: 123 minutes 10.77 seconds (7390.77 seconds total)