Starting phenix.real_space_refine on Mon Sep 14 05:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6i_21556/09_2026/6w6i_21556.map" } resolution = 3.5 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 68 5.16 5 C 17468 2.51 5 N 5138 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.03s 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: 28168 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: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 6.76, per 1000 atoms: 0.24 Number of scatterers: 28168 At special positions: 0 Unit cell: (137.472, 147.138, 134.25, 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 68 16.00 P 34 15.00 O 5460 8.00 N 5138 7.00 C 17468 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 26 sheets defined 53.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 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: 3.630A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.857A 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: 3.690A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 5.648A 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: 4.273A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.940A 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: 3.587A 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: 3.933A 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: 3.731A 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: 3.920A 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: 3.944A 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: 4.438A 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: 3.516A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.992A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.578A 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: 4.790A 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: 3.687A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) removed outlier: 3.577A 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: 5.244A 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: 3.888A 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: 3.610A 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: 3.507A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 469 removed outlier: 4.476A 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: 3.567A 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: 3.618A 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: 3.988A 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: 3.601A 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: 3.615A 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: 3.810A 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: 3.517A 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: 3.669A 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: 4.087A 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: 4.055A 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: 3.681A 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: 3.975A 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: 3.820A 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: 5.132A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.679A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.826A pdb=" N ILE D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.568A pdb=" N LEU D 232 " --> pdb=" O PRO D 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 229 through 233' Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.774A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.609A pdb=" N GLU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 5.343A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 removed outlier: 4.236A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 407 removed outlier: 3.871A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.840A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 624 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 641 through 649 removed outlier: 3.569A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.764A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 4.038A pdb=" N LEU D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 739 removed outlier: 3.529A pdb=" N LEU D 732 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA D 734 " --> pdb=" O GLN D 730 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 736 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 760 through 776 removed outlier: 3.781A pdb=" N ILE D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 804 through 806 No H-bonds generated for 'chain 'D' and resid 804 through 806' Processing helix chain 'D' and resid 807 through 815 Processing helix chain 'D' and resid 815 through 825 removed outlier: 3.929A pdb=" N ALA D 825 " --> pdb=" O LYS D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 184 through 194 removed outlier: 3.877A 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: 3.519A 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: 3.779A 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: 3.934A 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 170 through 175 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: 4.192A 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: 3.519A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 325 removed outlier: 3.910A 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: 5.530A 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: 3.851A 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: 3.919A 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: 3.879A 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: 3.528A 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: 3.677A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ASP F 697 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 3.662A 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: 3.678A pdb=" N ARG F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.952A 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: 6.992A pdb=" N ILE A 277 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.227A 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: 8.658A 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: 7.067A 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: 6.165A 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: 7.056A 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: 7.411A 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: 7.100A 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: 8.152A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 238 through 239 removed outlier: 6.802A pdb=" N THR D 275 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N ALA D 314 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE D 277 " --> pdb=" O ALA D 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 632 through 635 Processing sheet with id=AB8, first strand: chain 'D' and resid 700 through 701 removed outlier: 3.829A pdb=" N LEU D 701 " --> pdb=" O VAL D 709 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 782 through 784 Processing sheet with id=AC1, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC2, first strand: chain 'E' and resid 237 through 240 Processing sheet with id=AC3, 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=AC4, first strand: chain 'E' and resid 701 through 702 Processing sheet with id=AC5, 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=AC6, 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: 6.622A 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: 7.035A 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=AC7, first strand: chain 'F' and resid 700 through 702 Processing sheet with id=AC8, first strand: chain 'F' and resid 783 through 784 1119 hydrogen bonds defined for protein. 3162 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: 4.90 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 10113 1.37 - 1.51: 9129 1.51 - 1.66: 9180 1.66 - 1.80: 113 1.80 - 1.95: 13 Bond restraints: 28548 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 3.28e+01 bond pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " ideal model delta sigma weight residual 1.673 1.560 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" O3A AGS D 901 " pdb=" PA AGS D 901 " ideal model delta sigma weight residual 1.664 1.553 0.111 2.00e-02 2.50e+03 3.07e+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 3.04e+01 bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.563 0.110 2.00e-02 2.50e+03 3.00e+01 ... (remaining 28543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 38042 3.01 - 6.03: 454 6.03 - 9.04: 72 9.04 - 12.05: 27 12.05 - 15.07: 15 Bond angle restraints: 38610 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 113.53 105.06 8.47 9.80e-01 1.04e+00 7.47e+01 angle pdb=" N VAL E 801 " pdb=" CA VAL E 801 " pdb=" C VAL E 801 " ideal model delta sigma weight residual 113.53 106.16 7.37 9.80e-01 1.04e+00 5.66e+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 4.46e+01 angle pdb=" N ILE C 413 " pdb=" CA ILE C 413 " pdb=" C ILE C 413 " ideal model delta sigma weight residual 112.12 106.87 5.25 8.40e-01 1.42e+00 3.91e+01 angle pdb=" N VAL C 246 " pdb=" CA VAL C 246 " pdb=" C VAL C 246 " ideal model delta sigma weight residual 111.91 107.35 4.56 8.90e-01 1.26e+00 2.62e+01 ... (remaining 38605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 17266 35.75 - 71.50: 438 71.50 - 107.24: 91 107.24 - 142.99: 10 142.99 - 178.74: 19 Dihedral angle restraints: 17824 sinusoidal: 7547 harmonic: 10277 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 -117.79 -62.21 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 -141.17 -38.83 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 112.03 -172.03 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 17821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3727 0.068 - 0.136: 626 0.136 - 0.204: 29 0.204 - 0.272: 2 0.272 - 0.339: 8 Chirality restraints: 4392 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 2.88e+00 chirality pdb=" C3' AGS F 901 " pdb=" C2' AGS F 901 " pdb=" C4' AGS F 901 " pdb=" O3' AGS F 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.68 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C3' AGS D 901 " pdb=" C2' AGS D 901 " pdb=" C4' AGS D 901 " pdb=" O3' AGS D 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.68 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4389 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+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=" C LYS C 301 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 302 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 798 " 0.016 2.00e-02 2.50e+03 1.55e-02 4.22e+00 pdb=" CG PHE B 798 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 798 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 798 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 798 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 798 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 798 " 0.002 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 172 2.43 - 3.05: 18882 3.05 - 3.67: 39675 3.67 - 4.28: 58161 4.28 - 4.90: 97925 Nonbonded interactions: 214815 Sorted by model distance: 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 nonbonded pdb=" O1A ADP F 902 " pdb=" O3' ADP F 902 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR F 236 " pdb=" O GLN F 272 " model vdw 2.088 3.040 ... (remaining 214810 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.650 Find NCS groups from input model: 0.850 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 28552 Z= 0.573 Angle : 0.972 15.067 38610 Z= 0.507 Chirality : 0.050 0.339 4392 Planarity : 0.005 0.095 5056 Dihedral : 18.502 178.739 11196 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.16 % Favored : 86.67 % Rotamer: Outliers : 0.85 % Allowed : 9.06 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.12 % 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: -4.61 (0.12), residues: 3540 helix: -2.44 (0.10), residues: 1740 sheet: -3.11 (0.24), residues: 365 loop : -3.73 (0.13), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 418 TYR 0.012 0.002 TYR D 639 PHE 0.036 0.002 PHE B 798 TRP 0.030 0.002 TRP D 545 HIS 0.007 0.002 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.37 (28548) covalent geometry : angle 0.97165 / 0.51 (38610) hydrogen bonds : bond 0.18108 / 12.06 ( 1119) hydrogen bonds : angle 6.71388 / 4.72 ( 3162) Misc. bond : bond 0.37117 / 18.56 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 MET cc_start: 0.8305 (ttp) cc_final: 0.8079 (ttp) REVERT: D 685 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7602 (p90) REVERT: E 647 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7838 (ttm110) REVERT: F 310 ARG cc_start: 0.6792 (mmp-170) cc_final: 0.6304 (mmp80) REVERT: F 628 GLU cc_start: 0.8178 (tp30) cc_final: 0.7698 (tp30) outliers start: 25 outliers final: 23 residues processed: 272 average time/residue: 0.2373 time to fit residues: 94.6905 Evaluate side-chains 178 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 236 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 738 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: 358 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 268 ASN A 281 HIS A 323 HIS A 361 HIS A 795 GLN B 323 HIS B 335 GLN B 361 HIS B 643 HIS B 685 HIS B 705 HIS B 795 GLN B 813 GLN C 335 GLN C 575 GLN C 643 HIS C 663 GLN C 685 HIS C 778 GLN D 361 HIS D 643 HIS D 705 HIS D 827 GLN E 201 ASN E 685 HIS E 818 GLN F 298 ASN F 643 HIS F 685 HIS F 705 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075440 restraints weight = 70424.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077419 restraints weight = 38183.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078721 restraints weight = 25150.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079562 restraints weight = 19129.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080095 restraints weight = 16087.481| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28552 Z= 0.213 Angle : 0.721 11.435 38610 Z= 0.355 Chirality : 0.046 0.223 4392 Planarity : 0.005 0.085 5056 Dihedral : 16.765 179.129 4404 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.82 % Favored : 89.10 % Rotamer: Outliers : 1.92 % Allowed : 14.33 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.06 % 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: -3.28 (0.13), residues: 3540 helix: -1.27 (0.12), residues: 1772 sheet: -2.69 (0.24), residues: 392 loop : -3.14 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 563 TYR 0.012 0.001 TYR F 164 PHE 0.038 0.002 PHE D 798 TRP 0.025 0.002 TRP D 545 HIS 0.006 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (28548) covalent geometry : angle 0.72096 / 0.35 (38610) hydrogen bonds : bond 0.04470 / 2.96 ( 1119) hydrogen bonds : angle 5.13854 / 3.62 ( 3162) Misc. bond : bond 0.00207 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 393 ASP cc_start: 0.7880 (m-30) cc_final: 0.7675 (m-30) REVERT: B 564 MET cc_start: 0.8192 (ttp) cc_final: 0.7871 (ttp) REVERT: B 603 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.7706 (p90) REVERT: C 468 ASN cc_start: 0.7368 (p0) cc_final: 0.7165 (p0) REVERT: D 685 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (p90) REVERT: D 807 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8749 (tp) REVERT: E 245 MET cc_start: 0.1291 (mmt) cc_final: 0.0789 (mmt) REVERT: E 545 TRP cc_start: 0.8050 (m100) cc_final: 0.7805 (m100) REVERT: E 564 MET cc_start: 0.7659 (mmm) cc_final: 0.7436 (mmm) REVERT: E 647 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7793 (ttm110) REVERT: F 299 MET cc_start: 0.5362 (pmm) cc_final: 0.4861 (tpt) REVERT: F 310 ARG cc_start: 0.6748 (mmp-170) cc_final: 0.6390 (mmp80) REVERT: F 412 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: F 605 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6504 (p90) REVERT: F 628 GLU cc_start: 0.8107 (tp30) cc_final: 0.7694 (tp30) outliers start: 56 outliers final: 35 residues processed: 233 average time/residue: 0.1888 time to fit residues: 69.2073 Evaluate side-chains 194 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 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 603 PHE 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 166 THR Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 801 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 269 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 312 optimal weight: 30.0000 chunk 12 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 705 HIS C 361 HIS C 575 GLN E 201 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 818 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.077687 restraints weight = 70099.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079759 restraints weight = 39008.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081220 restraints weight = 22475.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081148 restraints weight = 18738.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081190 restraints weight = 17425.053| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28552 Z= 0.137 Angle : 0.618 9.597 38610 Z= 0.306 Chirality : 0.043 0.222 4392 Planarity : 0.005 0.081 5056 Dihedral : 15.038 178.824 4391 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.58 % Favored : 90.37 % Rotamer: Outliers : 2.09 % Allowed : 16.24 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -2.39 (0.14), residues: 3540 helix: -0.52 (0.13), residues: 1730 sheet: -2.37 (0.24), residues: 388 loop : -2.66 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 563 TYR 0.008 0.001 TYR B 655 PHE 0.037 0.001 PHE D 798 TRP 0.032 0.002 TRP F 545 HIS 0.010 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (28548) covalent geometry : angle 0.61779 / 0.31 (38610) hydrogen bonds : bond 0.03621 / 2.40 ( 1119) hydrogen bonds : angle 4.65966 / 3.30 ( 3162) Misc. bond : bond 0.00151 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.6867 (p90) REVERT: B 564 MET cc_start: 0.7989 (ttp) cc_final: 0.7602 (ttp) REVERT: C 327 ASP cc_start: 0.8222 (t0) cc_final: 0.7859 (t0) REVERT: E 299 MET cc_start: 0.8201 (tmm) cc_final: 0.7801 (tmm) REVERT: E 545 TRP cc_start: 0.8002 (m100) cc_final: 0.7740 (m100) REVERT: E 647 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7832 (ttm110) REVERT: F 299 MET cc_start: 0.5599 (pmm) cc_final: 0.4905 (tpt) REVERT: F 310 ARG cc_start: 0.6719 (mmp-170) cc_final: 0.6422 (mmp80) REVERT: F 324 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8102 (tp) REVERT: F 338 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: F 405 GLU cc_start: 0.8452 (pt0) cc_final: 0.8199 (pt0) REVERT: F 412 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: F 628 GLU cc_start: 0.8039 (tp30) cc_final: 0.7806 (tp30) REVERT: F 754 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6828 (pp20) outliers start: 61 outliers final: 36 residues processed: 236 average time/residue: 0.1889 time to fit residues: 70.1404 Evaluate side-chains 197 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 533 VAL 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 783 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 103 optimal weight: 0.4980 chunk 284 optimal weight: 10.0000 chunk 228 optimal weight: 0.0020 chunk 278 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 214 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 83 optimal weight: 0.0020 chunk 216 optimal weight: 0.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS B 452 GLN E 818 GLN E 829 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.075938 restraints weight = 69137.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078011 restraints weight = 36446.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079358 restraints weight = 23517.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080228 restraints weight = 17606.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080679 restraints weight = 14663.634| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28552 Z= 0.100 Angle : 0.567 9.403 38610 Z= 0.280 Chirality : 0.041 0.224 4392 Planarity : 0.004 0.077 5056 Dihedral : 14.387 177.836 4386 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 2.22 % Allowed : 17.03 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.92 (0.14), residues: 3540 helix: -0.18 (0.13), residues: 1739 sheet: -2.16 (0.25), residues: 384 loop : -2.37 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 401 TYR 0.008 0.001 TYR B 655 PHE 0.029 0.001 PHE D 798 TRP 0.039 0.001 TRP F 545 HIS 0.015 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (28548) covalent geometry : angle 0.56739 / 0.28 (38610) hydrogen bonds : bond 0.02963 / 1.97 ( 1119) hydrogen bonds : angle 4.34187 / 3.09 ( 3162) Misc. bond : bond 0.00191 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8695 (mt) cc_final: 0.8421 (mp) REVERT: A 603 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.6745 (p90) REVERT: B 564 MET cc_start: 0.7959 (ttp) cc_final: 0.7379 (ttp) REVERT: B 603 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7452 (p90) REVERT: B 605 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8536 (p90) REVERT: C 327 ASP cc_start: 0.8117 (t0) cc_final: 0.7542 (t70) REVERT: D 217 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: E 545 TRP cc_start: 0.7903 (m100) cc_final: 0.7670 (m100) REVERT: E 647 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7737 (ttm110) REVERT: F 259 LEU cc_start: 0.8474 (mm) cc_final: 0.7914 (pp) REVERT: F 310 ARG cc_start: 0.6450 (mmp-170) cc_final: 0.6217 (mmp80) REVERT: F 324 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8093 (tp) REVERT: F 338 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: F 405 GLU cc_start: 0.8447 (pt0) cc_final: 0.8144 (pt0) REVERT: F 412 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: F 754 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6696 (pt0) outliers start: 65 outliers final: 27 residues processed: 237 average time/residue: 0.1826 time to fit residues: 68.2480 Evaluate side-chains 189 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE 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 783 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 604 MET Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 14 optimal weight: 10.0000 chunk 227 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 0.5980 chunk 336 optimal weight: 0.0030 chunk 38 optimal weight: 0.9980 chunk 298 optimal weight: 0.0470 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.076944 restraints weight = 69224.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079025 restraints weight = 36764.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080380 restraints weight = 23727.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081256 restraints weight = 17783.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.081735 restraints weight = 14815.685| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 28552 Z= 0.099 Angle : 0.561 9.654 38610 Z= 0.275 Chirality : 0.041 0.262 4392 Planarity : 0.004 0.079 5056 Dihedral : 14.082 177.176 4384 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.79 % Favored : 91.16 % Rotamer: Outliers : 2.63 % Allowed : 17.37 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.48 (0.15), residues: 3540 helix: 0.14 (0.13), residues: 1726 sheet: -2.04 (0.25), residues: 386 loop : -2.03 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 462 TYR 0.008 0.001 TYR B 655 PHE 0.034 0.001 PHE D 798 TRP 0.061 0.002 TRP F 545 HIS 0.007 0.001 HIS E 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (28548) covalent geometry : angle 0.56088 / 0.28 (38610) hydrogen bonds : bond 0.02801 / 1.86 ( 1119) hydrogen bonds : angle 4.16857 / 2.98 ( 3162) Misc. bond : bond 0.00179 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.109 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 409 ARG cc_start: 0.7425 (ptp90) cc_final: 0.7123 (ptp90) REVERT: A 603 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.6776 (p90) REVERT: B 441 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7318 (mtm180) REVERT: B 564 MET cc_start: 0.7952 (ttp) cc_final: 0.7472 (ttp) REVERT: B 605 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8504 (p90) REVERT: C 327 ASP cc_start: 0.8122 (t0) cc_final: 0.7529 (t70) REVERT: D 217 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: E 299 MET cc_start: 0.7910 (tmm) cc_final: 0.7582 (tmm) REVERT: E 545 TRP cc_start: 0.7902 (m100) cc_final: 0.7672 (m100) REVERT: E 647 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7675 (ttm110) REVERT: F 259 LEU cc_start: 0.8460 (mm) cc_final: 0.7908 (pp) REVERT: F 310 ARG cc_start: 0.6573 (mmp-170) cc_final: 0.6284 (mmp80) REVERT: F 324 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8055 (tp) REVERT: F 338 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: F 405 GLU cc_start: 0.8522 (pt0) cc_final: 0.8214 (pt0) REVERT: F 412 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: F 754 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6742 (pt0) outliers start: 77 outliers final: 40 residues processed: 252 average time/residue: 0.1692 time to fit residues: 69.1870 Evaluate side-chains 211 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 605 PHE 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 701 LEU Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 824 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 244 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 301 optimal weight: 0.4980 chunk 348 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076018 restraints weight = 69511.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.078068 restraints weight = 36800.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079400 restraints weight = 23921.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080258 restraints weight = 18005.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080817 restraints weight = 15076.156| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 28552 Z= 0.112 Angle : 0.577 13.653 38610 Z= 0.281 Chirality : 0.042 0.259 4392 Planarity : 0.004 0.084 5056 Dihedral : 13.972 178.451 4381 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 2.80 % Allowed : 17.51 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.28 (0.15), residues: 3540 helix: 0.32 (0.13), residues: 1727 sheet: -1.97 (0.25), residues: 392 loop : -1.94 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 791 TYR 0.012 0.001 TYR F 658 PHE 0.027 0.001 PHE D 798 TRP 0.077 0.002 TRP F 545 HIS 0.007 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (28548) covalent geometry : angle 0.57746 / 0.28 (38610) hydrogen bonds : bond 0.02935 / 1.95 ( 1119) hydrogen bonds : angle 4.16302 / 2.98 ( 3162) Misc. bond : bond 0.00177 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 169 time to evaluate : 1.095 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 409 ARG cc_start: 0.7399 (ptp90) cc_final: 0.7109 (ptp90) REVERT: A 603 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6971 (p90) REVERT: B 441 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7490 (mtm180) REVERT: B 564 MET cc_start: 0.8119 (ttp) cc_final: 0.7602 (ttp) REVERT: B 603 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7738 (p90) REVERT: B 605 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8492 (p90) REVERT: C 327 ASP cc_start: 0.8263 (t0) cc_final: 0.7633 (t70) REVERT: C 465 ASN cc_start: 0.7654 (m-40) cc_final: 0.7383 (t0) REVERT: D 217 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: D 827 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: E 299 MET cc_start: 0.7924 (tmm) cc_final: 0.7564 (tmm) REVERT: E 545 TRP cc_start: 0.7924 (m100) cc_final: 0.7698 (m100) REVERT: E 564 MET cc_start: 0.7364 (mmm) cc_final: 0.7037 (mmm) REVERT: E 647 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7707 (ttm110) REVERT: F 259 LEU cc_start: 0.8486 (mm) cc_final: 0.7919 (pp) REVERT: F 277 ILE cc_start: 0.9114 (mm) cc_final: 0.8898 (tt) REVERT: F 310 ARG cc_start: 0.6640 (mmp-170) cc_final: 0.6342 (mmp80) REVERT: F 324 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8031 (tp) REVERT: F 338 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: F 405 GLU cc_start: 0.8576 (pt0) cc_final: 0.8289 (pt0) REVERT: F 412 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: F 605 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6336 (p90) REVERT: F 754 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6668 (pt0) outliers start: 82 outliers final: 53 residues processed: 240 average time/residue: 0.1785 time to fit residues: 69.0545 Evaluate side-chains 219 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE 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 701 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 207 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 605 PHE 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 754 GLU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 332 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 221 GLN B 705 HIS B 812 GLN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.071616 restraints weight = 69792.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073577 restraints weight = 37384.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.074896 restraints weight = 24564.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075710 restraints weight = 18648.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076281 restraints weight = 15704.280| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28552 Z= 0.229 Angle : 0.698 15.296 38610 Z= 0.340 Chirality : 0.046 0.280 4392 Planarity : 0.005 0.093 5056 Dihedral : 14.294 178.447 4381 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.83 % Favored : 90.08 % Rotamer: Outliers : 3.45 % Allowed : 18.19 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.56 (0.14), residues: 3540 helix: 0.10 (0.13), residues: 1753 sheet: -2.00 (0.24), residues: 410 loop : -2.18 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 775 TYR 0.011 0.001 TYR C 639 PHE 0.023 0.002 PHE D 798 TRP 0.053 0.002 TRP F 545 HIS 0.010 0.002 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (28548) covalent geometry : angle 0.69804 / 0.34 (38610) hydrogen bonds : bond 0.04121 / 2.72 ( 1119) hydrogen bonds : angle 4.59757 / 3.26 ( 3162) Misc. bond : bond 0.00183 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 143 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7143 (p90) REVERT: B 441 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7482 (mtm180) REVERT: B 564 MET cc_start: 0.8377 (ttp) cc_final: 0.7965 (ttp) REVERT: B 603 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7586 (p90) REVERT: D 217 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 827 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: E 299 MET cc_start: 0.8043 (tmm) cc_final: 0.7631 (tmm) REVERT: E 545 TRP cc_start: 0.8035 (m100) cc_final: 0.7810 (m100) REVERT: E 647 ARG cc_start: 0.8287 (ttp80) cc_final: 0.7802 (ttm110) REVERT: F 277 ILE cc_start: 0.9192 (mm) cc_final: 0.8842 (tt) REVERT: F 299 MET cc_start: 0.6038 (pmm) cc_final: 0.5061 (tpt) REVERT: F 310 ARG cc_start: 0.6719 (mmp-170) cc_final: 0.6510 (mmp80) REVERT: F 324 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8046 (tp) REVERT: F 338 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: F 405 GLU cc_start: 0.8662 (pt0) cc_final: 0.8426 (pt0) REVERT: F 412 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: F 605 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6544 (p90) REVERT: F 754 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6897 (pp20) outliers start: 101 outliers final: 69 residues processed: 236 average time/residue: 0.1755 time to fit residues: 67.4835 Evaluate side-chains 216 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 138 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 603 PHE 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 701 LEU Chi-restraints excluded: chain B residue 705 HIS 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 207 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 656 VAL 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 754 GLU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 250 optimal weight: 0.0170 chunk 222 optimal weight: 0.7980 chunk 347 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 323 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 705 HIS ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.098972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075782 restraints weight = 69234.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077871 restraints weight = 36351.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079241 restraints weight = 23424.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080129 restraints weight = 17571.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080700 restraints weight = 14620.782| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 28552 Z= 0.103 Angle : 0.585 11.926 38610 Z= 0.286 Chirality : 0.042 0.241 4392 Planarity : 0.004 0.081 5056 Dihedral : 13.956 175.543 4381 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.19 % Favored : 91.75 % Rotamer: Outliers : 2.12 % Allowed : 19.43 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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 (0.15), residues: 3540 helix: 0.42 (0.13), residues: 1743 sheet: -1.94 (0.24), residues: 409 loop : -1.95 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 791 TYR 0.010 0.001 TYR B 658 PHE 0.034 0.001 PHE D 798 TRP 0.057 0.002 TRP F 545 HIS 0.007 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (28548) covalent geometry : angle 0.58505 / 0.29 (38610) hydrogen bonds : bond 0.02871 / 1.91 ( 1119) hydrogen bonds : angle 4.19326 / 3.00 ( 3162) Misc. bond : bond 0.00170 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 ARG cc_start: 0.7561 (ptp90) cc_final: 0.7207 (ptp90) REVERT: A 603 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.6963 (p90) REVERT: B 245 MET cc_start: 0.8416 (mtp) cc_final: 0.8207 (ttm) REVERT: B 564 MET cc_start: 0.8022 (ttp) cc_final: 0.7436 (ttp) REVERT: C 327 ASP cc_start: 0.8142 (t0) cc_final: 0.7600 (t70) REVERT: D 217 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: D 230 GLU cc_start: 0.7007 (mp0) cc_final: 0.6779 (mp0) REVERT: D 827 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: E 299 MET cc_start: 0.7896 (tmm) cc_final: 0.7515 (tmm) REVERT: E 545 TRP cc_start: 0.7876 (m100) cc_final: 0.7664 (m100) REVERT: E 564 MET cc_start: 0.7605 (mmm) cc_final: 0.7318 (mmm) REVERT: E 647 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7721 (ttm110) REVERT: F 299 MET cc_start: 0.6154 (pmm) cc_final: 0.4995 (tpt) REVERT: F 324 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7854 (tp) REVERT: F 338 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: F 405 GLU cc_start: 0.8496 (pt0) cc_final: 0.8230 (pt0) REVERT: F 412 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: F 742 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7447 (mm-30) REVERT: F 754 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6674 (pt0) outliers start: 62 outliers final: 41 residues processed: 216 average time/residue: 0.1731 time to fit residues: 60.5875 Evaluate side-chains 199 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP 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 701 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 238 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 322 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 chunk 317 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.097634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.074637 restraints weight = 69558.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076681 restraints weight = 36719.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.078010 restraints weight = 23876.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078886 restraints weight = 18005.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.079446 restraints weight = 15013.113| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28552 Z= 0.126 Angle : 0.596 11.130 38610 Z= 0.290 Chirality : 0.042 0.215 4392 Planarity : 0.004 0.086 5056 Dihedral : 13.943 179.480 4381 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.93 % Favored : 91.02 % Rotamer: Outliers : 2.46 % Allowed : 19.32 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -1.09 (0.15), residues: 3540 helix: 0.51 (0.13), residues: 1737 sheet: -1.88 (0.24), residues: 411 loop : -1.91 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 462 TYR 0.008 0.001 TYR B 655 PHE 0.033 0.001 PHE D 798 TRP 0.057 0.002 TRP F 545 HIS 0.007 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (28548) covalent geometry : angle 0.59628 / 0.29 (38610) hydrogen bonds : bond 0.03151 / 2.09 ( 1119) hydrogen bonds : angle 4.22037 / 3.01 ( 3162) Misc. bond : bond 0.00178 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 146 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7029 (p90) REVERT: B 564 MET cc_start: 0.8104 (ttp) cc_final: 0.7625 (ttp) REVERT: C 327 ASP cc_start: 0.8181 (t0) cc_final: 0.7633 (t70) REVERT: D 217 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: D 827 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: E 564 MET cc_start: 0.7614 (mmm) cc_final: 0.7334 (mmm) REVERT: E 647 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7748 (ttm110) REVERT: F 299 MET cc_start: 0.6336 (pmm) cc_final: 0.4891 (tpt) REVERT: F 324 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7930 (tp) REVERT: F 338 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: F 405 GLU cc_start: 0.8523 (pt0) cc_final: 0.8279 (pt0) REVERT: F 412 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: F 605 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.6418 (p90) REVERT: F 754 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6669 (pt0) outliers start: 72 outliers final: 48 residues processed: 211 average time/residue: 0.1637 time to fit residues: 56.6146 Evaluate side-chains 198 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP 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 701 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 207 GLU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 406 ILE Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 13 optimal weight: 0.0010 chunk 157 optimal weight: 0.0980 chunk 220 optimal weight: 0.0370 chunk 236 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 ASN B 812 GLN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.100198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.077360 restraints weight = 69059.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079442 restraints weight = 36343.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080783 restraints weight = 23559.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081651 restraints weight = 17682.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082217 restraints weight = 14747.790| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 28552 Z= 0.097 Angle : 0.580 10.354 38610 Z= 0.281 Chirality : 0.042 0.215 4392 Planarity : 0.004 0.079 5056 Dihedral : 13.794 178.337 4379 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.22 % Favored : 91.72 % Rotamer: Outliers : 1.88 % Allowed : 19.84 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -0.87 (0.15), residues: 3540 helix: 0.69 (0.13), residues: 1732 sheet: -1.79 (0.25), residues: 402 loop : -1.79 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 462 TYR 0.008 0.001 TYR B 655 PHE 0.033 0.001 PHE D 798 TRP 0.061 0.002 TRP F 545 HIS 0.007 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (28548) covalent geometry : angle 0.58024 / 0.28 (38610) hydrogen bonds : bond 0.02677 / 1.78 ( 1119) hydrogen bonds : angle 4.06198 / 2.91 ( 3162) Misc. bond : bond 0.00185 / 0.09 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.6941 (p90) REVERT: B 564 MET cc_start: 0.8014 (ttp) cc_final: 0.7436 (ttp) REVERT: C 327 ASP cc_start: 0.8002 (t0) cc_final: 0.7441 (t70) REVERT: D 217 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: D 827 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: E 564 MET cc_start: 0.7631 (mmm) cc_final: 0.7346 (mmm) REVERT: E 647 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7707 (ttm110) REVERT: F 259 LEU cc_start: 0.8366 (mm) cc_final: 0.7873 (pp) REVERT: F 277 ILE cc_start: 0.9234 (mm) cc_final: 0.9024 (tt) REVERT: F 324 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7917 (tp) REVERT: F 338 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: F 405 GLU cc_start: 0.8545 (pt0) cc_final: 0.8269 (pt0) REVERT: F 412 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: F 754 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6502 (pt0) outliers start: 55 outliers final: 40 residues processed: 213 average time/residue: 0.1730 time to fit residues: 59.8204 Evaluate side-chains 197 residues out of total 2925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 461 THR 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 701 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 238 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 824 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 102 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 ASN ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076517 restraints weight = 68974.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078564 restraints weight = 36582.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079922 restraints weight = 23787.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.080788 restraints weight = 17820.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081340 restraints weight = 14877.126| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 28552 Z= 0.106 Angle : 0.584 10.813 38610 Z= 0.282 Chirality : 0.042 0.210 4392 Planarity : 0.004 0.083 5056 Dihedral : 13.779 179.115 4379 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.62 % Favored : 91.33 % Rotamer: Outliers : 1.71 % Allowed : 20.08 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -0.81 (0.15), residues: 3540 helix: 0.75 (0.13), residues: 1735 sheet: -1.67 (0.25), residues: 406 loop : -1.81 (0.17), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 462 TYR 0.009 0.001 TYR B 655 PHE 0.032 0.001 PHE D 798 TRP 0.057 0.001 TRP F 545 HIS 0.007 0.001 HIS F 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (28548) covalent geometry : angle 0.58372 / 0.28 (38610) hydrogen bonds : bond 0.02807 / 1.87 ( 1119) hydrogen bonds : angle 4.07684 / 2.90 ( 3162) Misc. bond : bond 0.00194 / 0.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.27 seconds wall clock time: 71 minutes 20.95 seconds (4280.95 seconds total)