Starting phenix.real_space_refine on Mon Sep 14 05:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6h_21555/09_2026/6w6h_21555_neut.cif" } resolution = 3.3 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 69 5.16 5 C 17630 2.51 5 N 5185 2.21 5 O 5509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 181 residue(s): 0.02s 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: 28427 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: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4872 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 24, 'TRANS': 604} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 4918 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 611} 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: 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: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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} Time building chain proxies: 6.99, per 1000 atoms: 0.25 Number of scatterers: 28427 At special positions: 0 Unit cell: (134.25, 154.656, 136.398, 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 69 16.00 P 34 15.00 O 5509 8.00 N 5185 7.00 C 17630 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6686 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 23 sheets defined 53.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.556A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.841A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 4.047A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.734A pdb=" N MET A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.785A pdb=" N SER A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.649A pdb=" N VAL A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 317 through 324 removed outlier: 4.332A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.586A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 333' Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.815A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.638A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.689A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.652A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 469 removed outlier: 3.616A pdb=" N LEU A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 4.002A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.649A pdb=" N LYS A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.857A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 621 removed outlier: 3.952A pdb=" N ALA A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.752A pdb=" N MET A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.543A pdb=" N VAL A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 691 through 696 removed outlier: 4.038A pdb=" N VAL A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'A' and resid 761 through 777 removed outlier: 3.776A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 786 through 796 removed outlier: 3.950A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 796 " --> pdb=" O TRP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.564A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 825 removed outlier: 3.715A pdb=" N LEU A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.689A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.917A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.629A pdb=" N ARG B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.843A pdb=" N GLU B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.841A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 Processing helix chain 'B' and resid 318 through 324 removed outlier: 3.544A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 removed outlier: 3.829A pdb=" N ALA B 328 " --> pdb=" O GLU B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 343 through 362 removed outlier: 5.297A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 378 Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.576A pdb=" N ARG B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 477 removed outlier: 4.029A pdb=" N ARG B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.560A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 567 through 571 Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.720A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.674A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 3.641A pdb=" N VAL B 645 " --> pdb=" O LYS B 642 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.593A pdb=" N ALA B 684 " --> pdb=" O ILE B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 728 through 739 removed outlier: 3.563A pdb=" N VAL B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 777 removed outlier: 4.439A pdb=" N ARG B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 764 " --> pdb=" O GLU B 760 " (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 797 removed outlier: 4.065A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 826 removed outlier: 3.514A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.595A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.526A pdb=" N ARG C 233 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.901A pdb=" N VAL C 284 " --> pdb=" O HIS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.571A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.664A pdb=" N ARG C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 317 through 322' Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.803A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.728A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 367 through 378 removed outlier: 3.608A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 removed outlier: 3.600A pdb=" N GLU C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 476 removed outlier: 3.926A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 544 Processing helix chain 'C' and resid 557 through 563 Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.787A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 624 removed outlier: 3.592A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 3.811A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 647 " --> pdb=" O THR C 644 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 649 " --> pdb=" O ALA C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 680 through 684 removed outlier: 3.648A pdb=" N ALA C 684 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 697 removed outlier: 4.074A pdb=" N ASP C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 739 removed outlier: 3.847A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.777A 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 759 through 777 removed outlier: 3.843A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 796 removed outlier: 3.957A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 824 removed outlier: 3.886A pdb=" N ARG C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.733A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.653A pdb=" N ILE D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.835A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 245 removed outlier: 3.578A pdb=" N MET D 245 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.884A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.244A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY D 285 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.828A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 324 removed outlier: 4.073A pdb=" N ARG D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.723A pdb=" N PHE D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 355 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 367 through 381 removed outlier: 3.960A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 407 removed outlier: 3.649A 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 removed outlier: 3.562A pdb=" N LYS D 560 " --> pdb=" O GLY D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 569 Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.806A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 626 Processing helix chain 'D' and resid 641 through 648 removed outlier: 3.568A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.726A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 693 removed outlier: 3.866A pdb=" N LEU D 692 " --> pdb=" O VAL D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 739 removed outlier: 3.614A pdb=" N ALA D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 760 through 776 removed outlier: 3.828A 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 806 through 825 removed outlier: 4.395A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 175 removed outlier: 3.639A pdb=" N ARG E 173 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY E 175 " --> pdb=" O ARG E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 169 through 175' Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.711A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 removed outlier: 3.687A pdb=" N ALA E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 256 through 270 Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 316 through 323 removed outlier: 3.602A pdb=" N LYS E 322 " --> pdb=" O ASP E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 343 through 354 Processing helix chain 'E' and resid 355 through 360 removed outlier: 3.807A pdb=" N VAL E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 382 removed outlier: 4.073A pdb=" N LEU E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 391 Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.891A pdb=" N ASP E 407 " --> pdb=" O MET E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 547 removed outlier: 4.712A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 removed outlier: 3.625A pdb=" N GLY E 569 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 589 removed outlier: 3.728A pdb=" N SER E 589 " --> pdb=" O ALA E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 625 Processing helix chain 'E' and resid 641 through 649 removed outlier: 5.534A pdb=" N ALA E 646 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 670 removed outlier: 4.086A pdb=" N ARG E 670 " --> pdb=" O GLU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 684 removed outlier: 3.520A pdb=" N LYS E 683 " --> pdb=" O GLU E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 696 removed outlier: 3.798A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 739 removed outlier: 3.917A pdb=" N LEU E 732 " --> pdb=" O ALA E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 747 Processing helix chain 'E' and resid 757 through 774 removed outlier: 3.973A pdb=" N VAL E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG E 763 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 764 " --> pdb=" O GLU E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 796 Processing helix chain 'E' and resid 806 through 826 removed outlier: 3.847A pdb=" N GLN E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE E 815 " --> pdb=" O VAL E 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 removed outlier: 4.373A pdb=" N ILE F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 226 removed outlier: 3.625A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 removed outlier: 3.583A pdb=" N LEU F 232 " --> pdb=" O PRO F 229 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 233 " --> pdb=" O GLU F 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 233' Processing helix chain 'F' and resid 253 through 269 removed outlier: 4.001A pdb=" N SER F 269 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.726A pdb=" N ILE F 283 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY F 285 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 305 Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.630A pdb=" N ARG F 321 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS F 322 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 removed outlier: 4.001A pdb=" N GLU F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 327 through 332' Processing helix chain 'F' and resid 343 through 355 Processing helix chain 'F' and resid 356 through 362 removed outlier: 3.622A pdb=" N VAL F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 378 removed outlier: 3.661A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 408 removed outlier: 3.585A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER F 408 " --> pdb=" O MET F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 431 removed outlier: 3.695A pdb=" N GLU F 417 " --> pdb=" O ILE F 413 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 425 " --> pdb=" O ARG F 421 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 426 " --> pdb=" O ARG F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 469 removed outlier: 4.181A pdb=" N ARG F 441 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 545 removed outlier: 3.652A pdb=" N ALA F 544 " --> pdb=" O ASP F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.670A pdb=" N THR F 558 " --> pdb=" O LEU F 554 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS F 560 " --> pdb=" O GLY F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 569 Processing helix chain 'F' and resid 575 through 591 removed outlier: 3.657A pdb=" N ALA F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 590 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 591 " --> pdb=" O ARG F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 625 removed outlier: 3.841A pdb=" N ALA F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 644 Processing helix chain 'F' and resid 645 through 650 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 663 through 670 removed outlier: 4.150A pdb=" N ALA F 667 " --> pdb=" O GLN F 663 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL F 668 " --> pdb=" O LEU F 664 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 687 through 693 Processing helix chain 'F' and resid 694 through 696 No H-bonds generated for 'chain 'F' and resid 694 through 696' Processing helix chain 'F' and resid 728 through 739 Processing helix chain 'F' and resid 740 through 745 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 796 removed outlier: 4.038A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 804 through 824 removed outlier: 3.964A pdb=" N ARG F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 809 " --> pdb=" O ARG F 805 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.700A pdb=" N ALA A 239 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 275 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ALA A 314 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 277 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N THR A 316 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 313 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 206 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 203 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 7.212A 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 602 through 606 removed outlier: 3.632A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 720 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 783 through 785 removed outlier: 3.642A pdb=" N VAL A 836 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.565A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 273 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL B 312 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 275 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ALA B 314 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE B 277 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N THR B 316 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 206 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 203 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 632 through 635 removed outlier: 6.332A pdb=" N GLY B 601 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N LEU B 718 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE B 603 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N SER B 720 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE B 605 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 782 through 785 removed outlier: 6.875A pdb=" N GLN B 782 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL B 836 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN B 784 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N VAL B 838 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 165 through 167 removed outlier: 3.573A pdb=" N ALA C 239 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP C 278 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 275 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ALA C 314 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE C 277 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.175A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.553A pdb=" N ILE C 634 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY C 601 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU C 718 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE C 603 " --> pdb=" O LEU C 718 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N SER C 720 " --> pdb=" O PHE C 603 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE C 605 " --> pdb=" O SER C 720 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 701 through 702 removed outlier: 3.691A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.002A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 238 through 239 removed outlier: 6.308A pdb=" N VAL D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP D 278 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR D 275 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ALA D 314 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE D 277 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N THR D 316 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR D 315 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU D 204 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL D 203 " --> pdb=" O VAL D 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 632 through 634 removed outlier: 5.771A pdb=" N VAL D 676 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR D 719 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE D 678 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE D 603 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N SER D 720 " --> pdb=" O PHE D 603 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE D 605 " --> pdb=" O SER D 720 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AB7, first strand: chain 'D' and resid 783 through 784 removed outlier: 3.533A pdb=" N GLN D 784 " --> pdb=" O VAL D 834 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 237 through 240 removed outlier: 4.752A pdb=" N ASP E 278 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 275 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA E 314 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 277 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR E 315 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU E 204 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 605 through 606 removed outlier: 7.104A pdb=" N PHE E 605 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP E 679 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE E 634 " --> pdb=" O ASP E 679 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 700 through 702 Processing sheet with id=AC2, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.326A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL F 312 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR F 275 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ALA F 314 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE F 277 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N THR F 316 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 206 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL F 203 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 632 through 635 removed outlier: 3.526A pdb=" N ILE F 634 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 679 " --> pdb=" O ILE F 634 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY F 601 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU F 718 " --> pdb=" O GLY F 601 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE F 603 " --> pdb=" O LEU F 718 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N SER F 720 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE F 605 " --> pdb=" O SER F 720 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 700 through 702 Processing sheet with id=AC5, first strand: chain 'F' and resid 782 through 785 removed outlier: 6.462A pdb=" N GLN F 782 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL F 836 " --> pdb=" O GLN F 782 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN F 784 " --> pdb=" O VAL F 836 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 1112 hydrogen bonds defined for protein. 3159 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: 5.87 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 11235 1.39 - 1.56: 17395 1.56 - 1.73: 51 1.73 - 1.90: 118 1.90 - 2.07: 10 Bond restraints: 28809 Sorted by residual: bond pdb=" PG AGS F 901 " pdb=" S1G AGS F 901 " ideal model delta sigma weight residual 1.936 2.074 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" PG AGS F 902 " pdb=" S1G AGS F 902 " ideal model delta sigma weight residual 1.936 2.073 -0.137 2.00e-02 2.50e+03 4.73e+01 bond pdb=" O3B AGS C 902 " pdb=" PB AGS C 902 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3B AGS A 901 " pdb=" PB AGS A 901 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" O3B AGS B 901 " pdb=" PB AGS B 901 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 28804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 38297 2.66 - 5.31: 536 5.31 - 7.97: 77 7.97 - 10.63: 40 10.63 - 13.29: 9 Bond angle restraints: 38959 Sorted by residual: angle pdb=" C LEU D 756 " pdb=" N ASN D 757 " pdb=" CA ASN D 757 " ideal model delta sigma weight residual 121.17 134.46 -13.29 1.62e+00 3.81e-01 6.73e+01 angle pdb=" N VAL A 593 " pdb=" CA VAL A 593 " pdb=" C VAL A 593 " ideal model delta sigma weight residual 113.47 108.26 5.21 1.01e+00 9.80e-01 2.66e+01 angle pdb=" N ILE C 413 " pdb=" CA ILE C 413 " pdb=" C ILE C 413 " ideal model delta sigma weight residual 112.96 108.38 4.58 1.00e+00 1.00e+00 2.10e+01 angle pdb=" N ALA C 429 " pdb=" CA ALA C 429 " pdb=" C ALA C 429 " ideal model delta sigma weight residual 114.75 109.01 5.74 1.26e+00 6.30e-01 2.08e+01 angle pdb=" N VAL C 593 " pdb=" CA VAL C 593 " pdb=" C VAL C 593 " ideal model delta sigma weight residual 113.71 109.44 4.27 9.50e-01 1.11e+00 2.02e+01 ... (remaining 38954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 17310 34.52 - 69.04: 553 69.04 - 103.56: 91 103.56 - 138.08: 15 138.08 - 172.60: 16 Dihedral angle restraints: 17985 sinusoidal: 7613 harmonic: 10372 Sorted by residual: dihedral pdb=" CA LEU C 387 " pdb=" C LEU C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 145.23 34.77 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA LEU D 387 " pdb=" C LEU D 387 " pdb=" N PRO D 388 " pdb=" CA PRO D 388 " ideal model delta harmonic sigma weight residual 180.00 146.06 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" O2A ADP E 902 " pdb=" O3A ADP E 902 " pdb=" PA ADP E 902 " pdb=" PB ADP E 902 " ideal model delta sinusoidal sigma weight residual -60.00 62.19 -122.19 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 17982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3576 0.056 - 0.112: 754 0.112 - 0.167: 86 0.167 - 0.223: 7 0.223 - 0.279: 8 Chirality restraints: 4431 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 -2.65 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' AGS B 902 " pdb=" C2' AGS B 902 " pdb=" C4' AGS B 902 " pdb=" O3' AGS B 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' AGS D 902 " pdb=" C2' AGS D 902 " pdb=" C4' AGS D 902 " pdb=" O3' AGS D 902 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4428 not shown) Planarity restraints: 5102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " -0.056 5.00e-02 4.00e+02 8.48e-02 1.15e+01 pdb=" N PRO B 388 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 387 " -0.056 5.00e-02 4.00e+02 8.42e-02 1.14e+01 pdb=" N PRO C 388 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 387 " -0.052 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO D 388 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 388 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 388 " -0.043 5.00e-02 4.00e+02 ... (remaining 5099 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.75: 6 1.75 - 2.54: 227 2.54 - 3.32: 34358 3.32 - 4.11: 62774 4.11 - 4.90: 119531 Warning: very small nonbonded interaction distances. Nonbonded interactions: 216896 Sorted by model distance: nonbonded pdb=" O VAL C 411 " pdb=" OE1 GLU C 412 " model vdw 0.962 3.040 nonbonded pdb=" C VAL C 411 " pdb=" OE1 GLU C 412 " model vdw 0.983 3.270 nonbonded pdb=" OE2 GLU C 426 " pdb=" NH1 ARG D 352 " model vdw 1.139 3.120 nonbonded pdb=" O GLU C 424 " pdb=" SD MET C 428 " model vdw 1.154 3.400 nonbonded pdb=" O VAL C 411 " pdb=" CD GLU C 412 " model vdw 1.688 3.270 ... (remaining 216891 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 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'B' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'C' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'D' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'E' and resid 159 through 845) selection = (chain 'F' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.180 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.090 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 0.006 0.460 28810 Z= 0.389 Angle : 0.870 13.287 38959 Z= 0.487 Chirality : 0.046 0.279 4431 Planarity : 0.005 0.085 5102 Dihedral : 18.500 172.605 11299 Min Nonbonded Distance : 0.962 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.87 % Favored : 89.94 % Rotamer: Outliers : 1.39 % Allowed : 5.80 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.10 % 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: -4.10 (0.12), residues: 3577 helix: -2.08 (0.11), residues: 1718 sheet: -3.08 (0.22), residues: 371 loop : -3.32 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 598 TYR 0.011 0.001 TYR B 655 PHE 0.016 0.002 PHE C 605 TRP 0.022 0.001 TRP E 545 HIS 0.004 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.28 (28809) covalent geometry : angle 0.87002 / 0.49 (38959) hydrogen bonds : bond 0.18187 / 12.08 ( 1112) hydrogen bonds : angle 6.31545 / 4.50 ( 3159) Misc. bond : bond 0.46041 / 24.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 1.139 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 327 ASP cc_start: 0.8341 (t0) cc_final: 0.7925 (t0) REVERT: A 331 GLU cc_start: 0.7819 (pp20) cc_final: 0.7552 (tm-30) REVERT: A 412 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: E 281 HIS cc_start: 0.7747 (p90) cc_final: 0.7036 (p90) REVERT: F 241 ASP cc_start: 0.7716 (t0) cc_final: 0.7426 (t0) REVERT: F 245 MET cc_start: 0.7261 (ttm) cc_final: 0.6362 (tpp) REVERT: F 462 ARG cc_start: 0.5967 (tmt170) cc_final: 0.5272 (tpt90) REVERT: F 629 ARG cc_start: 0.8070 (ptp-110) cc_final: 0.7831 (ptp-170) outliers start: 41 outliers final: 26 residues processed: 315 average time/residue: 0.2515 time to fit residues: 116.6775 Evaluate side-chains 176 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 453 LYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 738 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 overall best weight: 2.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 272 GLN B 643 HIS C 221 GLN ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN C 685 HIS C 730 GLN C 827 GLN D 643 HIS D 757 ASN D 827 GLN E 268 ASN ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 361 HIS E 745 ASN F 361 HIS F 643 HIS F 685 HIS F 818 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072245 restraints weight = 64147.265| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.03 r_work: 0.2864 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28810 Z= 0.228 Angle : 0.720 11.946 38959 Z= 0.353 Chirality : 0.046 0.250 4431 Planarity : 0.006 0.091 5102 Dihedral : 16.613 174.747 4476 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.46 % Favored : 89.46 % Rotamer: Outliers : 2.07 % Allowed : 12.68 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.10 % 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: -2.86 (0.14), residues: 3577 helix: -0.95 (0.12), residues: 1736 sheet: -2.73 (0.23), residues: 370 loop : -2.78 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 357 TYR 0.014 0.002 TYR A 358 PHE 0.032 0.002 PHE A 605 TRP 0.014 0.001 TRP F 463 HIS 0.007 0.001 HIS B 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (28809) covalent geometry : angle 0.71991 / 0.35 (38959) hydrogen bonds : bond 0.04716 / 3.23 ( 1112) hydrogen bonds : angle 4.80276 / 3.32 ( 3159) Misc. bond : bond 0.00167 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8967 (t0) cc_final: 0.8551 (t0) REVERT: A 331 GLU cc_start: 0.8396 (pp20) cc_final: 0.8059 (tm-30) REVERT: A 412 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: A 428 MET cc_start: 0.7637 (tmm) cc_final: 0.7267 (tmm) REVERT: A 627 ASP cc_start: 0.8769 (t0) cc_final: 0.8549 (t0) REVERT: B 603 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8615 (p90) REVERT: B 623 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8040 (p90) REVERT: C 412 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8720 (pm20) REVERT: C 433 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: D 747 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8859 (pp) REVERT: F 241 ASP cc_start: 0.7463 (t0) cc_final: 0.6900 (t0) REVERT: F 245 MET cc_start: 0.7265 (ttm) cc_final: 0.6027 (tpp) REVERT: F 303 MET cc_start: 0.7358 (mmm) cc_final: 0.7140 (mtt) REVERT: F 462 ARG cc_start: 0.4990 (tmt170) cc_final: 0.4637 (tmt170) REVERT: F 710 ASP cc_start: 0.8511 (p0) cc_final: 0.8165 (p0) outliers start: 61 outliers final: 35 residues processed: 215 average time/residue: 0.1922 time to fit residues: 66.9456 Evaluate side-chains 180 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 545 TRP Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 738 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 149 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 chunk 255 optimal weight: 0.0070 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 HIS B 361 HIS ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074790 restraints weight = 64033.130| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.98 r_work: 0.2925 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28810 Z= 0.126 Angle : 0.620 13.021 38959 Z= 0.300 Chirality : 0.042 0.173 4431 Planarity : 0.005 0.080 5102 Dihedral : 15.067 178.510 4441 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.67 % Favored : 91.25 % Rotamer: Outliers : 2.10 % Allowed : 14.31 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -2.12 (0.14), residues: 3577 helix: -0.32 (0.13), residues: 1734 sheet: -2.39 (0.24), residues: 367 loop : -2.43 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 357 TYR 0.014 0.001 TYR E 164 PHE 0.021 0.001 PHE A 605 TRP 0.011 0.001 TRP D 545 HIS 0.004 0.001 HIS C 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (28809) covalent geometry : angle 0.61960 / 0.30 (38959) hydrogen bonds : bond 0.03495 / 2.39 ( 1112) hydrogen bonds : angle 4.33501 / 2.97 ( 3159) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8842 (t0) cc_final: 0.8309 (t0) REVERT: A 331 GLU cc_start: 0.8365 (pp20) cc_final: 0.7979 (tm-30) REVERT: A 412 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: A 428 MET cc_start: 0.7648 (tmm) cc_final: 0.7220 (tmm) REVERT: A 627 ASP cc_start: 0.8715 (t0) cc_final: 0.8457 (t0) REVERT: B 331 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8748 (tm-30) REVERT: B 412 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 603 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8460 (p90) REVERT: B 623 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8060 (p90) REVERT: B 791 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7633 (mtm110) REVERT: C 430 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (tp) REVERT: C 433 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: D 562 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8847 (mm) REVERT: E 597 ASN cc_start: 0.8391 (m-40) cc_final: 0.7871 (p0) REVERT: E 798 PHE cc_start: 0.8543 (t80) cc_final: 0.8228 (t80) REVERT: F 241 ASP cc_start: 0.7527 (t0) cc_final: 0.6981 (t0) REVERT: F 245 MET cc_start: 0.7256 (ttm) cc_final: 0.5809 (tpp) REVERT: F 311 LEU cc_start: 0.8321 (tp) cc_final: 0.7977 (tt) REVERT: F 462 ARG cc_start: 0.4915 (tmt170) cc_final: 0.4705 (tmt170) REVERT: F 710 ASP cc_start: 0.8488 (p0) cc_final: 0.8129 (p0) outliers start: 62 outliers final: 21 residues processed: 218 average time/residue: 0.1766 time to fit residues: 64.2038 Evaluate side-chains 177 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 LYS Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 176 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 301 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 360 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 643 HIS ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.073931 restraints weight = 63429.690| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.86 r_work: 0.2917 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28810 Z= 0.131 Angle : 0.609 13.717 38959 Z= 0.295 Chirality : 0.042 0.164 4431 Planarity : 0.005 0.086 5102 Dihedral : 14.853 178.436 4433 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.09 % Favored : 90.86 % Rotamer: Outliers : 2.44 % Allowed : 16.01 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.77 (0.14), residues: 3577 helix: -0.05 (0.13), residues: 1734 sheet: -2.19 (0.24), residues: 371 loop : -2.24 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 357 TYR 0.011 0.001 TYR E 164 PHE 0.024 0.001 PHE A 605 TRP 0.010 0.001 TRP D 545 HIS 0.005 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (28809) covalent geometry : angle 0.60925 / 0.29 (38959) hydrogen bonds : bond 0.03398 / 2.33 ( 1112) hydrogen bonds : angle 4.16751 / 2.84 ( 3159) Misc. bond : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8862 (t0) cc_final: 0.8372 (t0) REVERT: A 331 GLU cc_start: 0.8342 (pp20) cc_final: 0.7955 (tm-30) REVERT: A 412 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: A 428 MET cc_start: 0.7561 (tmm) cc_final: 0.7130 (tmm) REVERT: A 606 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9032 (pp) REVERT: A 623 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7938 (p90) REVERT: A 627 ASP cc_start: 0.8716 (t0) cc_final: 0.8439 (t0) REVERT: B 331 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: B 412 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: B 603 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8405 (p90) REVERT: B 623 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8228 (p90) REVERT: C 428 MET cc_start: 0.8795 (tmm) cc_final: 0.8563 (tmm) REVERT: C 433 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: D 309 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (pp) REVERT: D 562 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 747 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8853 (pp) REVERT: E 597 ASN cc_start: 0.8396 (m-40) cc_final: 0.7880 (p0) REVERT: E 798 PHE cc_start: 0.8544 (t80) cc_final: 0.8274 (t80) REVERT: F 165 SER cc_start: 0.7912 (m) cc_final: 0.7497 (t) REVERT: F 238 VAL cc_start: 0.7702 (m) cc_final: 0.7377 (p) REVERT: F 241 ASP cc_start: 0.7804 (t0) cc_final: 0.7223 (t0) REVERT: F 245 MET cc_start: 0.7176 (ttm) cc_final: 0.5980 (tpp) REVERT: F 311 LEU cc_start: 0.8347 (tp) cc_final: 0.7995 (tt) REVERT: F 444 LYS cc_start: 0.7491 (mtpp) cc_final: 0.7128 (tmtt) REVERT: F 710 ASP cc_start: 0.8580 (p0) cc_final: 0.8217 (p0) outliers start: 72 outliers final: 40 residues processed: 221 average time/residue: 0.1791 time to fit residues: 65.6283 Evaluate side-chains 197 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 545 TRP Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 40 optimal weight: 0.8980 chunk 349 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 271 optimal weight: 8.9990 chunk 306 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 745 ASN F 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.100666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.073867 restraints weight = 63470.071| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.81 r_work: 0.2928 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28810 Z= 0.126 Angle : 0.595 15.234 38959 Z= 0.288 Chirality : 0.042 0.169 4431 Planarity : 0.005 0.079 5102 Dihedral : 14.686 178.148 4427 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.92 % Favored : 91.03 % Rotamer: Outliers : 2.48 % Allowed : 16.92 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.52 (0.15), residues: 3577 helix: 0.16 (0.13), residues: 1735 sheet: -2.09 (0.24), residues: 382 loop : -2.12 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 357 TYR 0.012 0.001 TYR E 164 PHE 0.023 0.001 PHE A 605 TRP 0.010 0.001 TRP D 545 HIS 0.006 0.001 HIS F 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (28809) covalent geometry : angle 0.59462 / 0.29 (38959) hydrogen bonds : bond 0.03241 / 2.22 ( 1112) hydrogen bonds : angle 4.06741 / 2.78 ( 3159) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 168 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8875 (t0) cc_final: 0.8374 (t0) REVERT: A 331 GLU cc_start: 0.8342 (pp20) cc_final: 0.7969 (tm-30) REVERT: A 428 MET cc_start: 0.7554 (tmm) cc_final: 0.7110 (tmm) REVERT: A 606 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 623 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7927 (p90) REVERT: A 627 ASP cc_start: 0.8710 (t0) cc_final: 0.8429 (t0) REVERT: B 331 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8890 (tm-30) REVERT: B 603 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8426 (p90) REVERT: B 623 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8175 (p90) REVERT: B 791 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7558 (mtm110) REVERT: C 428 MET cc_start: 0.8816 (tmm) cc_final: 0.8529 (tmm) REVERT: C 433 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: C 623 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7840 (p90) REVERT: D 309 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8704 (pp) REVERT: D 562 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8878 (mm) REVERT: D 747 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8860 (pp) REVERT: E 597 ASN cc_start: 0.8416 (m-40) cc_final: 0.7860 (p0) REVERT: E 798 PHE cc_start: 0.8534 (t80) cc_final: 0.8261 (t80) REVERT: F 165 SER cc_start: 0.7876 (m) cc_final: 0.7643 (t) REVERT: F 241 ASP cc_start: 0.7831 (t0) cc_final: 0.7305 (t0) REVERT: F 245 MET cc_start: 0.7194 (ttm) cc_final: 0.5858 (tpp) REVERT: F 311 LEU cc_start: 0.8295 (tp) cc_final: 0.7948 (tt) REVERT: F 444 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7183 (tmtt) REVERT: F 455 LYS cc_start: 0.7233 (tppt) cc_final: 0.6972 (tppt) REVERT: F 459 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.5125 (mm) REVERT: F 462 ARG cc_start: 0.5272 (tmt170) cc_final: 0.5025 (tpt90) REVERT: F 682 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: F 710 ASP cc_start: 0.8614 (p0) cc_final: 0.8263 (p0) outliers start: 73 outliers final: 43 residues processed: 230 average time/residue: 0.1817 time to fit residues: 69.1533 Evaluate side-chains 207 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 545 TRP Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 682 GLU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 84 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 255 optimal weight: 0.0040 chunk 173 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 132 optimal weight: 0.0980 chunk 345 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 342 optimal weight: 1.9990 overall best weight: 0.8294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 685 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.101635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.074885 restraints weight = 63179.870| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.81 r_work: 0.2951 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28810 Z= 0.103 Angle : 0.567 15.295 38959 Z= 0.275 Chirality : 0.041 0.258 4431 Planarity : 0.005 0.082 5102 Dihedral : 14.597 179.307 4427 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 2.44 % Allowed : 17.46 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.28 (0.15), residues: 3577 helix: 0.35 (0.13), residues: 1731 sheet: -1.96 (0.24), residues: 382 loop : -1.99 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 357 TYR 0.012 0.001 TYR E 164 PHE 0.019 0.001 PHE A 605 TRP 0.011 0.001 TRP D 545 HIS 0.004 0.001 HIS F 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (28809) covalent geometry : angle 0.56720 / 0.27 (38959) hydrogen bonds : bond 0.02879 / 1.98 ( 1112) hydrogen bonds : angle 3.95094 / 2.69 ( 3159) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 164 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8701 (pt0) cc_final: 0.8148 (pt0) REVERT: A 327 ASP cc_start: 0.8834 (t0) cc_final: 0.8315 (t0) REVERT: A 331 GLU cc_start: 0.8319 (pp20) cc_final: 0.7966 (tm-30) REVERT: A 428 MET cc_start: 0.7520 (tmm) cc_final: 0.7061 (tmm) REVERT: A 606 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9015 (pp) REVERT: A 623 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7805 (p90) REVERT: A 627 ASP cc_start: 0.8660 (t0) cc_final: 0.8363 (t0) REVERT: B 331 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.8944 (tm-30) REVERT: B 603 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8373 (p90) REVERT: B 791 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7550 (mtm110) REVERT: B 827 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: C 412 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: C 428 MET cc_start: 0.8761 (tmm) cc_final: 0.8458 (tmm) REVERT: C 433 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: C 623 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7774 (p90) REVERT: C 641 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8577 (mm-30) REVERT: D 309 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8642 (pp) REVERT: D 552 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7646 (tmm-80) REVERT: D 562 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8873 (mm) REVERT: D 747 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8856 (pp) REVERT: E 597 ASN cc_start: 0.8421 (m-40) cc_final: 0.7892 (p0) REVERT: E 798 PHE cc_start: 0.8534 (t80) cc_final: 0.8289 (t80) REVERT: F 165 SER cc_start: 0.7797 (m) cc_final: 0.7486 (t) REVERT: F 238 VAL cc_start: 0.7554 (m) cc_final: 0.7020 (p) REVERT: F 241 ASP cc_start: 0.7845 (t0) cc_final: 0.7344 (t0) REVERT: F 245 MET cc_start: 0.7294 (ttm) cc_final: 0.6093 (tpp) REVERT: F 311 LEU cc_start: 0.8239 (tp) cc_final: 0.7917 (tt) REVERT: F 444 LYS cc_start: 0.7524 (mtpp) cc_final: 0.7160 (tmtt) REVERT: F 455 LYS cc_start: 0.7325 (tppt) cc_final: 0.7101 (tppt) REVERT: F 459 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.5042 (mm) REVERT: F 710 ASP cc_start: 0.8567 (p0) cc_final: 0.8209 (p0) outliers start: 72 outliers final: 39 residues processed: 225 average time/residue: 0.1835 time to fit residues: 67.5881 Evaluate side-chains 197 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 603 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 813 GLN Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 117 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 334 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 268 ASN F 694 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.075164 restraints weight = 63343.897| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.82 r_work: 0.2957 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28810 Z= 0.103 Angle : 0.566 15.632 38959 Z= 0.274 Chirality : 0.041 0.275 4431 Planarity : 0.005 0.076 5102 Dihedral : 14.424 178.688 4424 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 2.31 % Allowed : 18.28 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -1.12 (0.15), residues: 3577 helix: 0.48 (0.13), residues: 1731 sheet: -1.94 (0.24), residues: 387 loop : -1.87 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 563 TYR 0.013 0.001 TYR E 164 PHE 0.019 0.001 PHE A 605 TRP 0.009 0.001 TRP D 545 HIS 0.004 0.001 HIS F 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (28809) covalent geometry : angle 0.56617 / 0.27 (38959) hydrogen bonds : bond 0.02857 / 1.96 ( 1112) hydrogen bonds : angle 3.90723 / 2.66 ( 3159) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8694 (pt0) cc_final: 0.8130 (pt0) REVERT: A 327 ASP cc_start: 0.8824 (t0) cc_final: 0.8302 (t0) REVERT: A 331 GLU cc_start: 0.8306 (pp20) cc_final: 0.7967 (tm-30) REVERT: A 409 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7218 (ttm110) REVERT: A 428 MET cc_start: 0.7442 (tmm) cc_final: 0.6958 (tmm) REVERT: A 606 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 623 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (p90) REVERT: A 627 ASP cc_start: 0.8639 (t0) cc_final: 0.8347 (t0) REVERT: B 322 LYS cc_start: 0.9558 (ttpt) cc_final: 0.9303 (tttp) REVERT: B 331 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8978 (tm-30) REVERT: B 603 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8420 (p90) REVERT: B 791 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7539 (mtm110) REVERT: B 827 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: C 412 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: C 428 MET cc_start: 0.8744 (tmm) cc_final: 0.8447 (tmm) REVERT: C 623 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7782 (p90) REVERT: C 641 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: C 827 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: D 309 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8611 (pp) REVERT: D 552 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7681 (tmm-80) REVERT: D 562 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8884 (mm) REVERT: D 747 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8881 (pp) REVERT: D 798 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.6787 (t80) REVERT: E 798 PHE cc_start: 0.8496 (t80) cc_final: 0.8266 (t80) REVERT: F 165 SER cc_start: 0.7898 (m) cc_final: 0.7475 (t) REVERT: F 238 VAL cc_start: 0.7595 (m) cc_final: 0.7041 (p) REVERT: F 245 MET cc_start: 0.7127 (ttm) cc_final: 0.6230 (tpp) REVERT: F 311 LEU cc_start: 0.8044 (tp) cc_final: 0.7607 (tt) REVERT: F 444 LYS cc_start: 0.7541 (mtpp) cc_final: 0.7156 (tmtt) REVERT: F 455 LYS cc_start: 0.7231 (tppt) cc_final: 0.7003 (tppt) REVERT: F 459 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.5094 (mm) REVERT: F 462 ARG cc_start: 0.4713 (tmt170) cc_final: 0.4404 (tpt90) REVERT: F 710 ASP cc_start: 0.8551 (p0) cc_final: 0.8194 (p0) REVERT: F 732 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7813 (mm) outliers start: 68 outliers final: 43 residues processed: 222 average time/residue: 0.1852 time to fit residues: 67.6317 Evaluate side-chains 211 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 153 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 813 GLN Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 798 PHE Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 362 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 296 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 338 optimal weight: 0.0870 chunk 295 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN E 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074714 restraints weight = 63307.394| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.84 r_work: 0.2935 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28810 Z= 0.121 Angle : 0.575 15.105 38959 Z= 0.279 Chirality : 0.042 0.277 4431 Planarity : 0.005 0.081 5102 Dihedral : 14.358 179.492 4421 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.72 % Favored : 91.25 % Rotamer: Outliers : 2.54 % Allowed : 18.41 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3577 helix: 0.55 (0.13), residues: 1732 sheet: -1.85 (0.24), residues: 389 loop : -1.82 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 809 TYR 0.015 0.001 TYR E 164 PHE 0.022 0.001 PHE A 605 TRP 0.010 0.001 TRP D 545 HIS 0.004 0.001 HIS F 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (28809) covalent geometry : angle 0.57545 / 0.28 (38959) hydrogen bonds : bond 0.03021 / 2.07 ( 1112) hydrogen bonds : angle 3.91710 / 2.67 ( 3159) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 157 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8743 (pt0) cc_final: 0.8157 (pt0) REVERT: A 327 ASP cc_start: 0.8831 (t0) cc_final: 0.8322 (t0) REVERT: A 331 GLU cc_start: 0.8337 (pp20) cc_final: 0.7989 (tm-30) REVERT: A 409 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7266 (ttm110) REVERT: A 428 MET cc_start: 0.7540 (tmm) cc_final: 0.7035 (tmm) REVERT: A 606 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9012 (pp) REVERT: A 623 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7801 (p90) REVERT: A 627 ASP cc_start: 0.8669 (t0) cc_final: 0.8374 (t0) REVERT: B 322 LYS cc_start: 0.9552 (ttpt) cc_final: 0.9292 (tttp) REVERT: B 331 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9008 (tm-30) REVERT: B 603 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8482 (p90) REVERT: B 791 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7575 (mtm110) REVERT: B 827 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: C 412 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: C 428 MET cc_start: 0.8729 (tmm) cc_final: 0.8383 (tmm) REVERT: C 606 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (pp) REVERT: C 623 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7766 (p90) REVERT: C 641 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: C 827 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: D 390 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8484 (ptmt) REVERT: D 552 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7715 (tmm-80) REVERT: D 562 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8776 (mm) REVERT: D 747 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8867 (pp) REVERT: D 798 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6835 (t80) REVERT: E 354 LEU cc_start: 0.9210 (mt) cc_final: 0.8991 (mt) REVERT: E 798 PHE cc_start: 0.8485 (t80) cc_final: 0.8253 (t80) REVERT: F 165 SER cc_start: 0.7665 (m) cc_final: 0.7279 (t) REVERT: F 238 VAL cc_start: 0.7640 (m) cc_final: 0.7081 (p) REVERT: F 241 ASP cc_start: 0.7822 (t0) cc_final: 0.7317 (t0) REVERT: F 245 MET cc_start: 0.7076 (ttm) cc_final: 0.5905 (tpp) REVERT: F 311 LEU cc_start: 0.8043 (tp) cc_final: 0.7614 (tt) REVERT: F 444 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7145 (tmtt) REVERT: F 455 LYS cc_start: 0.7156 (tppt) cc_final: 0.6939 (tppt) REVERT: F 459 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.5068 (mm) REVERT: F 462 ARG cc_start: 0.4712 (tmt170) cc_final: 0.4385 (tpt90) REVERT: F 710 ASP cc_start: 0.8544 (p0) cc_final: 0.8191 (p0) outliers start: 75 outliers final: 50 residues processed: 223 average time/residue: 0.1776 time to fit residues: 65.2186 Evaluate side-chains 217 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 152 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 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 623 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 813 GLN Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 798 PHE Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 362 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 118 optimal weight: 0.9980 chunk 330 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 260 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 34 optimal weight: 0.0270 chunk 346 optimal weight: 6.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075131 restraints weight = 63216.699| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.82 r_work: 0.2935 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28810 Z= 0.121 Angle : 0.579 15.360 38959 Z= 0.280 Chirality : 0.042 0.238 4431 Planarity : 0.005 0.076 5102 Dihedral : 14.302 178.624 4421 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.78 % Favored : 91.19 % Rotamer: Outliers : 2.54 % Allowed : 18.41 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -0.94 (0.15), residues: 3577 helix: 0.62 (0.13), residues: 1731 sheet: -1.67 (0.25), residues: 386 loop : -1.84 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 809 TYR 0.016 0.001 TYR E 164 PHE 0.021 0.001 PHE A 605 TRP 0.010 0.001 TRP D 545 HIS 0.004 0.001 HIS F 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (28809) covalent geometry : angle 0.57891 / 0.28 (38959) hydrogen bonds : bond 0.03033 / 2.08 ( 1112) hydrogen bonds : angle 3.91519 / 2.67 ( 3159) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 151 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8725 (pt0) cc_final: 0.8147 (pt0) REVERT: A 327 ASP cc_start: 0.8840 (t0) cc_final: 0.8339 (t0) REVERT: A 331 GLU cc_start: 0.8342 (pp20) cc_final: 0.8006 (tm-30) REVERT: A 409 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7284 (ttm110) REVERT: A 428 MET cc_start: 0.7612 (tmm) cc_final: 0.7093 (tmm) REVERT: A 606 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9022 (pp) REVERT: A 623 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7781 (p90) REVERT: A 627 ASP cc_start: 0.8678 (t0) cc_final: 0.8381 (t0) REVERT: B 322 LYS cc_start: 0.9554 (ttpt) cc_final: 0.9291 (tttp) REVERT: B 331 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9031 (tm-30) REVERT: B 603 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8437 (p90) REVERT: B 791 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7584 (mtm110) REVERT: B 827 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: C 428 MET cc_start: 0.8728 (tmm) cc_final: 0.8378 (tmm) REVERT: C 606 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8988 (pp) REVERT: C 623 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7800 (p90) REVERT: C 641 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8581 (mm-30) REVERT: C 827 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: D 390 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8483 (ptmt) REVERT: D 552 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7712 (tmm-80) REVERT: D 562 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8849 (mm) REVERT: D 747 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8866 (pp) REVERT: D 798 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6846 (t80) REVERT: E 354 LEU cc_start: 0.9219 (mt) cc_final: 0.9012 (mt) REVERT: E 798 PHE cc_start: 0.8526 (t80) cc_final: 0.8287 (t80) REVERT: F 165 SER cc_start: 0.7550 (m) cc_final: 0.7185 (t) REVERT: F 238 VAL cc_start: 0.7661 (m) cc_final: 0.7191 (p) REVERT: F 245 MET cc_start: 0.7100 (ttm) cc_final: 0.6152 (tpp) REVERT: F 311 LEU cc_start: 0.8059 (tp) cc_final: 0.7624 (tt) REVERT: F 455 LYS cc_start: 0.7223 (tppt) cc_final: 0.7008 (tppt) REVERT: F 459 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5141 (mm) REVERT: F 462 ARG cc_start: 0.4900 (tmt170) cc_final: 0.4519 (tpt90) REVERT: F 710 ASP cc_start: 0.8535 (p0) cc_final: 0.8179 (p0) outliers start: 75 outliers final: 53 residues processed: 216 average time/residue: 0.1619 time to fit residues: 58.9780 Evaluate side-chains 215 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 148 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 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 623 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 813 GLN Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 798 PHE Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 362 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 105 optimal weight: 3.9990 chunk 232 optimal weight: 0.0370 chunk 333 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 252 optimal weight: 0.3980 chunk 255 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 HIS E 201 ASN F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.074137 restraints weight = 63075.806| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.82 r_work: 0.2913 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 28810 Z= 0.149 Angle : 0.602 14.865 38959 Z= 0.293 Chirality : 0.043 0.297 4431 Planarity : 0.005 0.082 5102 Dihedral : 14.338 177.362 4421 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.89 % Favored : 91.08 % Rotamer: Outliers : 2.37 % Allowed : 18.65 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -0.95 (0.15), residues: 3577 helix: 0.62 (0.13), residues: 1732 sheet: -1.64 (0.25), residues: 386 loop : -1.86 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 779 TYR 0.016 0.001 TYR E 164 PHE 0.025 0.002 PHE A 605 TRP 0.011 0.001 TRP D 545 HIS 0.004 0.001 HIS D 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (28809) covalent geometry : angle 0.60214 / 0.29 (38959) hydrogen bonds : bond 0.03328 / 2.29 ( 1112) hydrogen bonds : angle 3.98634 / 2.72 ( 3159) Misc. bond : bond 0.00081 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7154 Ramachandran restraints generated. 3577 Oldfield, 0 Emsley, 3577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 145 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8894 (t0) cc_final: 0.8451 (t0) REVERT: A 331 GLU cc_start: 0.8371 (pp20) cc_final: 0.8020 (tm-30) REVERT: A 409 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7252 (ttm110) REVERT: A 428 MET cc_start: 0.7670 (tmm) cc_final: 0.7134 (tmm) REVERT: A 606 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 623 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7898 (p90) REVERT: A 627 ASP cc_start: 0.8718 (t0) cc_final: 0.8405 (t0) REVERT: B 322 LYS cc_start: 0.9556 (ttpt) cc_final: 0.9288 (tttp) REVERT: B 331 GLU cc_start: 0.9426 (OUTLIER) cc_final: 0.9051 (tm-30) REVERT: B 603 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8454 (p90) REVERT: B 791 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7563 (mtm110) REVERT: B 827 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: C 428 MET cc_start: 0.8754 (tmm) cc_final: 0.8378 (tmm) REVERT: C 606 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9007 (pp) REVERT: C 623 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7798 (p90) REVERT: C 641 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8585 (mm-30) REVERT: C 827 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: D 390 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8483 (ptmt) REVERT: D 552 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7709 (tmm-80) REVERT: D 562 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8826 (mm) REVERT: D 747 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8859 (pp) REVERT: D 798 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6795 (t80) REVERT: E 798 PHE cc_start: 0.8488 (t80) cc_final: 0.8255 (t80) REVERT: F 165 SER cc_start: 0.7603 (m) cc_final: 0.7265 (t) REVERT: F 238 VAL cc_start: 0.7692 (m) cc_final: 0.7232 (p) REVERT: F 245 MET cc_start: 0.7103 (ttm) cc_final: 0.6081 (tpp) REVERT: F 311 LEU cc_start: 0.8066 (tp) cc_final: 0.7618 (tt) REVERT: F 455 LYS cc_start: 0.7189 (tppt) cc_final: 0.6981 (tppt) REVERT: F 459 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5132 (mm) REVERT: F 462 ARG cc_start: 0.4919 (tmt170) cc_final: 0.4536 (tpt90) REVERT: F 552 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7026 (ptm160) REVERT: F 710 ASP cc_start: 0.8552 (p0) cc_final: 0.8196 (p0) outliers start: 70 outliers final: 50 residues processed: 205 average time/residue: 0.1764 time to fit residues: 60.2472 Evaluate side-chains 208 residues out of total 2950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 MET Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 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 623 PHE Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 813 GLN Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain D residue 390 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 545 TRP Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 649 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 798 PHE Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 334 PHE Chi-restraints excluded: chain E residue 362 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 738 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 552 ARG Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 580 THR Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 623 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 738 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 246 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 325 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 0.0070 chunk 345 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN D 362 HIS E 201 ASN E 268 ASN E 281 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076133 restraints weight = 62912.550| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.84 r_work: 0.2962 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 28810 Z= 0.098 Angle : 0.567 15.898 38959 Z= 0.274 Chirality : 0.041 0.234 4431 Planarity : 0.004 0.075 5102 Dihedral : 14.184 178.982 4421 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.10 % Allowed : 18.85 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.40 % 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: -0.80 (0.15), residues: 3577 helix: 0.73 (0.13), residues: 1742 sheet: -1.60 (0.25), residues: 389 loop : -1.77 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 563 TYR 0.016 0.001 TYR E 164 PHE 0.016 0.001 PHE A 386 TRP 0.009 0.001 TRP D 545 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (28809) covalent geometry : angle 0.56669 / 0.27 (38959) hydrogen bonds : bond 0.02711 / 1.86 ( 1112) hydrogen bonds : angle 3.85367 / 2.61 ( 3159) Misc. bond : bond 0.00079 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5919.11 seconds wall clock time: 102 minutes 16.90 seconds (6136.90 seconds total)