Starting phenix.real_space_refine on Mon Sep 14 03:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w6g_21554/09_2026/6w6g_21554.cif" } resolution = 3.1 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 67 5.16 5 C 17109 2.51 5 N 5033 2.21 5 O 5338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27581 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4796 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 24, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4115 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 21, 'TRANS': 509} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.14, per 1000 atoms: 0.22 Number of scatterers: 27581 At special positions: 0 Unit cell: (137.472, 147.138, 135.324, 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 67 16.00 P 34 15.00 O 5338 8.00 N 5033 7.00 C 17109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6488 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 29 sheets defined 52.4% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.603A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.838A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.592A 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 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.750A pdb=" N SER A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 317 through 324 removed outlier: 3.736A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.580A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 5.035A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.755A pdb=" N LEU A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 391 through 407 removed outlier: 4.036A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 428 Processing helix chain 'A' and resid 437 through 469 removed outlier: 3.722A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 4.237A pdb=" N LYS A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 591 removed outlier: 3.515A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.700A pdb=" N LYS A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 642 through 648 removed outlier: 3.509A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.669A pdb=" N VAL A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.554A pdb=" N LEU A 692 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 761 through 776 Processing helix chain 'A' and resid 786 through 797 removed outlier: 3.928A pdb=" N GLY A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.702A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.939A pdb=" N TYR B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.640A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.729A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.777A pdb=" N ARG B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.505A pdb=" N ILE B 283 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.860A pdb=" N PHE B 334 " --> pdb=" O GLU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.887A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.566A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 3.586A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.684A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 429 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 469 removed outlier: 3.506A pdb=" N ARG B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 464 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 575 through 591 removed outlier: 4.118A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.896A pdb=" N ALA B 617 " --> pdb=" O LYS B 613 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 3.725A 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 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.545A pdb=" N GLU B 698 " --> pdb=" O GLN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 739 removed outlier: 3.637A pdb=" N VAL B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 761 through 777 removed outlier: 3.813A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 780 No H-bonds generated for 'chain 'B' and resid 778 through 780' Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.946A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 815 removed outlier: 4.030A pdb=" N ARG B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 824 removed outlier: 3.819A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.587A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.989A pdb=" N ARG C 233 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.735A pdb=" N SER C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.829A pdb=" N VAL C 284 " --> pdb=" O HIS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 307 removed outlier: 3.711A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.735A pdb=" N HIS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.635A pdb=" N PHE C 334 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.692A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 381 removed outlier: 3.562A pdb=" N LEU C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG C 380 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 391 through 407 removed outlier: 3.699A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.555A pdb=" N ARG C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 469 removed outlier: 3.904A pdb=" N ARG C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 464 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 557 through 569 removed outlier: 5.807A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 591 removed outlier: 3.723A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 626 removed outlier: 3.936A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 631 removed outlier: 3.971A pdb=" N MET C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 663 through 670 removed outlier: 3.833A pdb=" N ARG C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 684 removed outlier: 3.547A pdb=" N ALA C 684 " --> pdb=" O ILE C 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 681 through 684' Processing helix chain 'C' and resid 689 through 691 No H-bonds generated for 'chain 'C' and resid 689 through 691' Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 730 through 739 removed outlier: 3.744A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 777 removed outlier: 4.512A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 786 through 796 removed outlier: 3.777A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 824 removed outlier: 3.816A pdb=" N ARG C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.586A pdb=" N GLU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.738A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 removed outlier: 3.882A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.761A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.746A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.793A pdb=" N VAL D 284 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.928A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 362 removed outlier: 5.188A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 removed outlier: 4.206A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 407 removed outlier: 3.786A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.647A 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 557 through 563 Processing helix chain 'D' and resid 575 through 591 removed outlier: 3.707A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL D 582 " --> pdb=" O ALA D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 626 Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 641 through 648 removed outlier: 3.766A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.993A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 690 removed outlier: 3.634A pdb=" N ASP D 690 " --> pdb=" O ASP D 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 687 through 690' Processing helix chain 'D' and resid 691 through 696 Processing helix chain 'D' and resid 731 through 739 removed outlier: 3.552A pdb=" N VAL D 735 " --> pdb=" O VAL D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 760 through 776 Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 804 through 806 No H-bonds generated for 'chain 'D' and resid 804 through 806' Processing helix chain 'D' and resid 807 through 815 Processing helix chain 'D' and resid 815 through 825 Processing helix chain 'E' and resid 167 through 175 removed outlier: 3.747A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 194 Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 241 through 246 removed outlier: 3.772A pdb=" N MET E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 246' Processing helix chain 'E' and resid 254 through 270 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 316 through 324 Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.581A pdb=" N PHE E 334 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 354 Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 386 through 406 removed outlier: 4.051A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 547 removed outlier: 3.716A pdb=" N ALA E 539 " --> pdb=" O PRO E 535 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP E 540 " --> pdb=" O ASP E 536 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 590 Processing helix chain 'E' and resid 612 through 625 removed outlier: 3.502A pdb=" N LEU E 616 " --> pdb=" O GLY E 612 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 649 removed outlier: 3.810A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 670 removed outlier: 3.957A pdb=" N ARG E 670 " --> pdb=" O GLU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 680 through 684 removed outlier: 3.678A pdb=" N ALA E 684 " --> pdb=" O ILE E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 695 removed outlier: 3.766A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 739 removed outlier: 3.814A pdb=" N PHE E 739 " --> pdb=" O VAL E 735 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 745 removed outlier: 3.729A pdb=" N ILE E 744 " --> pdb=" O LYS E 740 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN E 745 " --> pdb=" O PRO E 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 740 through 745' Processing helix chain 'E' and resid 758 through 760 No H-bonds generated for 'chain 'E' and resid 758 through 760' Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 786 through 791 Processing helix chain 'E' and resid 791 through 799 removed outlier: 4.556A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP E 799 " --> pdb=" O GLN E 795 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 826 removed outlier: 4.424A pdb=" N ARG E 809 " --> pdb=" O ARG E 805 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL E 811 " --> pdb=" O LEU E 807 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS E 821 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N MET E 822 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 824 " --> pdb=" O ALA E 820 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.585A pdb=" N GLN F 162 " --> pdb=" O GLN F 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS F 163 " --> pdb=" O ALA F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 226 Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.533A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 307 Processing helix chain 'F' and resid 317 through 325 removed outlier: 3.755A pdb=" N GLU F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 367 through 377 removed outlier: 4.164A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 406 Processing helix chain 'F' and resid 534 through 544 Processing helix chain 'F' and resid 567 through 572 Processing helix chain 'F' and resid 575 through 590 Processing helix chain 'F' and resid 612 through 625 removed outlier: 3.664A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE F 625 " --> pdb=" O ALA F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 671 Processing helix chain 'F' and resid 685 through 696 removed outlier: 3.743A pdb=" N PHE F 689 " --> pdb=" O HIS F 685 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 690 " --> pdb=" O PRO F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 739 removed outlier: 3.773A pdb=" N LEU F 732 " --> pdb=" O ALA F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 760 Processing helix chain 'F' and resid 761 through 777 Processing helix chain 'F' and resid 778 through 780 No H-bonds generated for 'chain 'F' and resid 778 through 780' Processing helix chain 'F' and resid 786 through 797 removed outlier: 3.914A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG F 796 " --> pdb=" O TRP F 792 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 825 removed outlier: 4.343A pdb=" N LEU F 807 " --> pdb=" O GLY F 803 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 6.484A pdb=" N VAL A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP A 278 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 275 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA A 314 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A 277 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N THR A 316 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 206 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.871A 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: 7.387A pdb=" N ARG A 365 " --> pdb=" O VAL A 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 635 removed outlier: 6.949A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 603 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 720 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.510A pdb=" N GLN A 784 " --> pdb=" O VAL A 836 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL A 838 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.542A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 273 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N VAL B 312 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 275 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ALA B 314 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE B 277 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N THR B 316 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 206 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 203 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 339 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 205 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 365 through 366 removed outlier: 7.348A pdb=" N ARG B 365 " --> pdb=" O VAL B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 632 through 635 removed outlier: 7.088A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY B 601 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 718 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 603 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N SER B 720 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N PHE B 605 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 701 through 702 Processing sheet with id=AB1, first strand: chain 'B' and resid 837 through 838 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 3.714A pdb=" N ALA C 239 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.908A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY C 206 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 203 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 339 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 205 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.309A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.713A pdb=" N SER C 720 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 700 through 702 Processing sheet with id=AB7, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.199A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL C 838 " --> pdb=" O GLN C 784 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.438A pdb=" N VAL D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP D 278 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR D 275 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ALA D 314 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE D 277 " --> pdb=" O ALA D 314 " (cutoff:3.500A) removed outlier: 9.556A pdb=" N THR D 316 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 206 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL D 203 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 365 through 366 removed outlier: 7.199A pdb=" N ARG D 365 " --> pdb=" O VAL D 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.087A pdb=" N VAL D 676 " --> pdb=" O ILE D 717 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE D 603 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 701 through 702 Processing sheet with id=AC3, first strand: chain 'D' and resid 782 through 785 removed outlier: 4.283A pdb=" N VAL D 836 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.170A pdb=" N VAL E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR E 315 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU E 204 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 601 through 604 removed outlier: 6.080A pdb=" N GLY E 601 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU E 718 " --> pdb=" O GLY E 601 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE E 603 " --> pdb=" O LEU E 718 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 700 through 702 Processing sheet with id=AC7, first strand: chain 'F' and resid 313 through 316 Processing sheet with id=AC8, first strand: chain 'F' and resid 716 through 720 removed outlier: 9.103A pdb=" N LEU F 751 " --> pdb=" O ALA F 602 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET F 604 " --> pdb=" O LEU F 751 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 631 through 634 Processing sheet with id=AD1, first strand: chain 'F' and resid 782 through 784 Processing sheet with id=AD2, first strand: chain 'F' and resid 837 through 838 1076 hydrogen bonds defined for protein. 3099 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: 5.21 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 9771 1.37 - 1.51: 8222 1.51 - 1.66: 9836 1.66 - 1.80: 110 1.80 - 1.95: 14 Bond restraints: 27953 Sorted by residual: bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP E 902 " pdb=" C6 ADP E 902 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CA ALA B 621 " pdb=" C ALA B 621 " ideal model delta sigma weight residual 1.522 1.474 0.048 1.38e-02 5.25e+03 1.22e+01 bond pdb=" CA ALA A 621 " pdb=" C ALA A 621 " ideal model delta sigma weight residual 1.523 1.480 0.044 1.80e-02 3.09e+03 5.85e+00 bond pdb=" CA THR A 600 " pdb=" C THR A 600 " ideal model delta sigma weight residual 1.523 1.482 0.042 1.80e-02 3.09e+03 5.32e+00 ... (remaining 27948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 37150 2.42 - 4.85: 583 4.85 - 7.27: 61 7.27 - 9.69: 10 9.69 - 12.12: 5 Bond angle restraints: 37809 Sorted by residual: angle pdb=" N ILE A 413 " pdb=" CA ILE A 413 " pdb=" C ILE A 413 " ideal model delta sigma weight residual 111.90 106.25 5.65 8.10e-01 1.52e+00 4.87e+01 angle pdb=" N ASN B 298 " pdb=" CA ASN B 298 " pdb=" C ASN B 298 " ideal model delta sigma weight residual 114.39 107.20 7.19 1.45e+00 4.76e-01 2.46e+01 angle pdb=" N VAL F 210 " pdb=" CA VAL F 210 " pdb=" C VAL F 210 " ideal model delta sigma weight residual 113.71 109.06 4.65 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N VAL A 593 " pdb=" CA VAL A 593 " pdb=" C VAL A 593 " ideal model delta sigma weight residual 113.53 109.32 4.21 9.80e-01 1.04e+00 1.84e+01 angle pdb=" C ASN D 597 " pdb=" N ARG D 598 " pdb=" CA ARG D 598 " ideal model delta sigma weight residual 121.80 131.89 -10.09 2.44e+00 1.68e-01 1.71e+01 ... (remaining 37804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 16616 32.78 - 65.56: 499 65.56 - 98.33: 34 98.33 - 131.11: 2 131.11 - 163.89: 2 Dihedral angle restraints: 17153 sinusoidal: 7093 harmonic: 10060 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -116.09 -63.91 0 5.00e+00 4.00e-02 1.63e+02 dihedral pdb=" CA PHE C 386 " pdb=" C PHE C 386 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " ideal model delta harmonic sigma weight residual 180.00 -143.81 -36.19 0 5.00e+00 4.00e-02 5.24e+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 300.00 136.11 163.89 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 17150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2643 0.037 - 0.074: 1209 0.074 - 0.111: 364 0.111 - 0.148: 102 0.148 - 0.185: 10 Chirality restraints: 4328 Sorted by residual: chirality pdb=" CB ILE F 273 " pdb=" CA ILE F 273 " pdb=" CG1 ILE F 273 " pdb=" CG2 ILE F 273 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA LEU C 387 " pdb=" N LEU C 387 " pdb=" C LEU C 387 " pdb=" CB LEU C 387 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" PA AGS A 902 " pdb=" O2A AGS A 902 " pdb=" O3A AGS A 902 " pdb=" O5' AGS A 902 " both_signs ideal model delta sigma weight residual True 3.18 -3.02 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 4325 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 388 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 545 " -0.021 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 545 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 545 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 545 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 545 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 545 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 545 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 545 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 545 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 545 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 652 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO E 653 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 653 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 653 " 0.032 5.00e-02 4.00e+02 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 710 2.68 - 3.24: 27270 3.24 - 3.79: 39578 3.79 - 4.35: 54043 4.35 - 4.90: 90288 Nonbonded interactions: 211889 Sorted by model distance: nonbonded pdb=" O1B AGS B 902 " pdb=" O2G AGS B 902 " model vdw 2.131 3.040 nonbonded pdb=" OH TYR E 639 " pdb=" OE1 GLN E 663 " model vdw 2.132 3.040 nonbonded pdb=" O1B AGS A 901 " pdb=" O2G AGS A 901 " model vdw 2.150 3.040 nonbonded pdb=" O1B AGS D 902 " pdb=" O2G AGS D 902 " model vdw 2.168 3.040 nonbonded pdb=" O THR C 236 " pdb=" OG1 THR C 236 " model vdw 2.173 3.040 ... (remaining 211884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 650 or resid 663 through 901)) selection = (chain 'F' and resid 159 through 901) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.080 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.889 27957 Z= 0.711 Angle : 0.787 12.116 37809 Z= 0.450 Chirality : 0.046 0.185 4328 Planarity : 0.005 0.101 4946 Dihedral : 15.447 163.888 10665 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.52 % Favored : 88.31 % Rotamer: Outliers : 0.66 % Allowed : 7.23 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.09 % 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: -4.32 (0.12), residues: 3464 helix: -2.09 (0.11), residues: 1693 sheet: -3.21 (0.23), residues: 356 loop : -3.68 (0.13), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 222 TYR 0.022 0.002 TYR B 639 PHE 0.018 0.002 PHE C 386 TRP 0.044 0.002 TRP D 545 HIS 0.005 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (27953) covalent geometry : angle 0.78677 / 0.45 (37809) hydrogen bonds : bond 0.16437 / 10.85 ( 1076) hydrogen bonds : angle 6.26857 / 4.42 ( 3099) Misc. bond : bond 0.55813 / 27.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 278 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.5346 (p90) REVERT: A 631 MET cc_start: 0.9019 (ptt) cc_final: 0.8794 (ptt) REVERT: A 680 GLU cc_start: 0.8527 (mp0) cc_final: 0.8301 (mm-30) REVERT: B 421 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7253 (ttp-170) REVERT: B 427 GLU cc_start: 0.8018 (tt0) cc_final: 0.7653 (tm-30) REVERT: B 451 ASP cc_start: 0.8318 (m-30) cc_final: 0.7978 (m-30) REVERT: B 553 LEU cc_start: 0.8605 (mm) cc_final: 0.8391 (mt) REVERT: C 331 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 629 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8212 (mtm110) REVERT: D 404 MET cc_start: 0.8280 (mmm) cc_final: 0.7916 (tpp) REVERT: E 262 VAL cc_start: 0.9034 (t) cc_final: 0.8727 (p) REVERT: F 377 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6029 (pp) REVERT: F 670 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7711 (mmm-85) outliers start: 19 outliers final: 16 residues processed: 295 average time/residue: 0.2504 time to fit residues: 106.6454 Evaluate side-chains 189 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 833 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain B residue 833 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain F residue 377 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 361 HIS A 685 HIS B 361 HIS B 464 GLN B 468 ASN B 778 GLN B 813 GLN C 643 HIS C 663 GLN C 685 HIS C 812 GLN D 643 HIS D 705 HIS D 730 GLN D 827 GLN E 201 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 HIS E 768 GLN F 201 ASN F 757 ASN F 812 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080183 restraints weight = 50614.598| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.71 r_work: 0.2983 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27957 Z= 0.123 Angle : 0.657 14.980 37809 Z= 0.327 Chirality : 0.043 0.207 4328 Planarity : 0.005 0.083 4946 Dihedral : 8.868 131.550 4025 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.33 % Favored : 89.58 % Rotamer: Outliers : 1.15 % Allowed : 11.70 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -2.78 (0.14), residues: 3464 helix: -0.70 (0.13), residues: 1664 sheet: -2.80 (0.23), residues: 376 loop : -2.94 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 633 TYR 0.023 0.001 TYR F 639 PHE 0.025 0.001 PHE D 798 TRP 0.025 0.002 TRP D 545 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (27953) covalent geometry : angle 0.65722 / 0.33 (37809) hydrogen bonds : bond 0.03963 / 2.70 ( 1076) hydrogen bonds : angle 4.87324 / 3.46 ( 3099) Misc. bond : bond 0.00136 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.5847 (p90) REVERT: A 680 GLU cc_start: 0.8965 (mp0) cc_final: 0.8445 (mm-30) REVERT: B 331 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: B 427 GLU cc_start: 0.7592 (tt0) cc_final: 0.7076 (tm-30) REVERT: C 412 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7815 (pm20) REVERT: C 629 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8882 (mtm110) REVERT: D 404 MET cc_start: 0.8718 (mmm) cc_final: 0.8254 (tpp) REVERT: D 838 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8014 (t) REVERT: E 404 MET cc_start: 0.8106 (ttp) cc_final: 0.7898 (ttp) REVERT: F 323 HIS cc_start: 0.7571 (m90) cc_final: 0.7012 (m-70) REVERT: F 358 TYR cc_start: 0.7518 (p90) cc_final: 0.7001 (p90) REVERT: F 377 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6129 (pp) REVERT: F 387 LEU cc_start: 0.7548 (mt) cc_final: 0.7030 (tp) REVERT: F 396 ASP cc_start: 0.5628 (m-30) cc_final: 0.5419 (t0) REVERT: F 605 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5449 (p90) outliers start: 33 outliers final: 13 residues processed: 227 average time/residue: 0.2057 time to fit residues: 72.9118 Evaluate side-chains 187 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 779 ARG Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 749 ASP Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 188 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 229 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 chunk 217 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 228 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 705 HIS E 745 ASN E 768 GLN E 813 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080861 restraints weight = 50916.880| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.73 r_work: 0.2995 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27957 Z= 0.111 Angle : 0.602 14.607 37809 Z= 0.298 Chirality : 0.042 0.206 4328 Planarity : 0.004 0.081 4946 Dihedral : 8.322 132.622 4013 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.67 % Favored : 90.24 % Rotamer: Outliers : 1.78 % Allowed : 13.10 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3464 helix: -0.11 (0.13), residues: 1659 sheet: -2.44 (0.24), residues: 372 loop : -2.62 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 633 TYR 0.016 0.001 TYR F 639 PHE 0.023 0.001 PHE C 605 TRP 0.022 0.001 TRP D 545 HIS 0.003 0.001 HIS A 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (27953) covalent geometry : angle 0.60202 / 0.30 (37809) hydrogen bonds : bond 0.03501 / 2.36 ( 1076) hydrogen bonds : angle 4.58646 / 3.26 ( 3099) Misc. bond : bond 0.00174 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.5829 (p90) REVERT: A 680 GLU cc_start: 0.9010 (mp0) cc_final: 0.8451 (mm-30) REVERT: B 331 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8693 (tm-30) REVERT: B 427 GLU cc_start: 0.7497 (tt0) cc_final: 0.6991 (tm-30) REVERT: C 412 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: C 629 ARG cc_start: 0.9137 (mtm110) cc_final: 0.8893 (mtm110) REVERT: D 404 MET cc_start: 0.8733 (mmm) cc_final: 0.8271 (tpp) REVERT: D 552 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7763 (tmm-80) REVERT: D 712 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8628 (mmm-85) REVERT: E 257 GLU cc_start: 0.7655 (tt0) cc_final: 0.7225 (tm-30) REVERT: E 679 ASP cc_start: 0.7528 (m-30) cc_final: 0.7137 (m-30) REVERT: E 768 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: F 319 GLU cc_start: 0.7745 (tp30) cc_final: 0.7070 (mm-30) REVERT: F 323 HIS cc_start: 0.7518 (m90) cc_final: 0.6019 (m-70) REVERT: F 358 TYR cc_start: 0.7484 (p90) cc_final: 0.6977 (p90) REVERT: F 377 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6251 (pp) REVERT: F 387 LEU cc_start: 0.7662 (mt) cc_final: 0.7081 (tp) outliers start: 51 outliers final: 16 residues processed: 237 average time/residue: 0.1997 time to fit residues: 74.6516 Evaluate side-chains 194 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain E residue 768 GLN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 308 optimal weight: 0.0570 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 8.9990 chunk 221 optimal weight: 0.0570 chunk 214 optimal weight: 0.8980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS D 685 HIS E 813 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082496 restraints weight = 50411.264| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.72 r_work: 0.3027 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27957 Z= 0.097 Angle : 0.584 14.513 37809 Z= 0.286 Chirality : 0.042 0.210 4328 Planarity : 0.004 0.079 4946 Dihedral : 8.006 127.288 4012 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.32 % Favored : 90.62 % Rotamer: Outliers : 1.82 % Allowed : 14.04 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.69 (0.15), residues: 3464 helix: 0.20 (0.14), residues: 1659 sheet: -2.15 (0.24), residues: 382 loop : -2.43 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 805 TYR 0.025 0.001 TYR F 639 PHE 0.022 0.001 PHE D 798 TRP 0.020 0.001 TRP D 545 HIS 0.004 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (27953) covalent geometry : angle 0.58411 / 0.29 (37809) hydrogen bonds : bond 0.03046 / 2.06 ( 1076) hydrogen bonds : angle 4.42856 / 3.15 ( 3099) Misc. bond : bond 0.00188 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6459 (pt0) REVERT: A 623 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.5619 (p90) REVERT: A 680 GLU cc_start: 0.8995 (mp0) cc_final: 0.8423 (mm-30) REVERT: B 181 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9048 (mp) REVERT: B 331 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8703 (tm-30) REVERT: B 412 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: B 427 GLU cc_start: 0.7474 (tt0) cc_final: 0.7012 (tm-30) REVERT: C 412 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: C 629 ARG cc_start: 0.9134 (mtm110) cc_final: 0.8880 (mtm110) REVERT: D 404 MET cc_start: 0.8741 (mmm) cc_final: 0.8260 (tpp) REVERT: D 552 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7904 (tmm-80) REVERT: D 712 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8548 (mmm-85) REVERT: E 257 GLU cc_start: 0.7642 (tt0) cc_final: 0.7233 (tm-30) REVERT: E 564 MET cc_start: 0.7659 (mmm) cc_final: 0.7310 (mmm) REVERT: F 194 LEU cc_start: 0.8506 (tt) cc_final: 0.8144 (mt) REVERT: F 217 GLU cc_start: 0.8603 (pt0) cc_final: 0.8129 (tt0) REVERT: F 279 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7918 (tp30) REVERT: F 319 GLU cc_start: 0.7733 (tp30) cc_final: 0.7136 (mm-30) REVERT: F 323 HIS cc_start: 0.7584 (m90) cc_final: 0.6209 (m-70) REVERT: F 377 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6271 (pp) REVERT: F 387 LEU cc_start: 0.7761 (mt) cc_final: 0.7194 (tp) REVERT: F 605 PHE cc_start: 0.5927 (OUTLIER) cc_final: 0.5480 (p90) REVERT: F 670 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7371 (mmt-90) REVERT: F 827 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.5829 (pt0) outliers start: 52 outliers final: 17 residues processed: 230 average time/residue: 0.1960 time to fit residues: 72.0325 Evaluate side-chains 201 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 188 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 313 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 99 optimal weight: 0.0070 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS B 281 HIS E 813 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082948 restraints weight = 51408.178| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.45 r_work: 0.3013 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27957 Z= 0.100 Angle : 0.575 14.335 37809 Z= 0.281 Chirality : 0.042 0.211 4328 Planarity : 0.004 0.080 4946 Dihedral : 7.850 125.121 4009 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.24 % Favored : 90.70 % Rotamer: Outliers : 1.85 % Allowed : 14.88 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.40 (0.15), residues: 3464 helix: 0.44 (0.14), residues: 1661 sheet: -2.06 (0.24), residues: 392 loop : -2.27 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 332 TYR 0.014 0.001 TYR F 639 PHE 0.020 0.001 PHE D 798 TRP 0.021 0.001 TRP D 545 HIS 0.005 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (27953) covalent geometry : angle 0.57472 / 0.28 (37809) hydrogen bonds : bond 0.03044 / 2.07 ( 1076) hydrogen bonds : angle 4.32711 / 3.08 ( 3099) Misc. bond : bond 0.00134 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8315 (mmm160) REVERT: A 555 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: A 623 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.5835 (p90) REVERT: B 181 ILE cc_start: 0.9547 (OUTLIER) cc_final: 0.9128 (mp) REVERT: B 331 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8922 (tm-30) REVERT: B 412 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: B 427 GLU cc_start: 0.7718 (tt0) cc_final: 0.7201 (tm-30) REVERT: C 412 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: C 605 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8437 (p90) REVERT: C 629 ARG cc_start: 0.9269 (mtm110) cc_final: 0.9051 (mtm110) REVERT: D 404 MET cc_start: 0.8824 (mmm) cc_final: 0.8448 (tpp) REVERT: D 552 ARG cc_start: 0.8399 (ttp-170) cc_final: 0.8096 (tmm-80) REVERT: E 257 GLU cc_start: 0.7652 (tt0) cc_final: 0.7269 (tm-30) REVERT: E 564 MET cc_start: 0.7654 (mmm) cc_final: 0.7337 (mmm) REVERT: E 604 MET cc_start: 0.8435 (ppp) cc_final: 0.8056 (ppp) REVERT: E 813 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6497 (pp30) REVERT: F 194 LEU cc_start: 0.8648 (tt) cc_final: 0.8287 (mt) REVERT: F 217 GLU cc_start: 0.8637 (pt0) cc_final: 0.8095 (tt0) REVERT: F 279 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7982 (tp30) REVERT: F 319 GLU cc_start: 0.7782 (tp30) cc_final: 0.7166 (mm-30) REVERT: F 323 HIS cc_start: 0.7797 (m90) cc_final: 0.6460 (m-70) REVERT: F 377 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6339 (pp) REVERT: F 387 LEU cc_start: 0.7708 (mt) cc_final: 0.7181 (tp) REVERT: F 670 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7459 (mmt-90) REVERT: F 827 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5573 (pt0) outliers start: 53 outliers final: 25 residues processed: 228 average time/residue: 0.1983 time to fit residues: 71.9018 Evaluate side-chains 209 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 813 GLN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 241 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 81 optimal weight: 0.0270 chunk 261 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 322 optimal weight: 0.0980 chunk 43 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083406 restraints weight = 51751.344| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.52 r_work: 0.3001 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27957 Z= 0.112 Angle : 0.575 14.382 37809 Z= 0.283 Chirality : 0.042 0.204 4328 Planarity : 0.004 0.081 4946 Dihedral : 7.811 123.424 4009 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 1.75 % Allowed : 15.44 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.24 (0.15), residues: 3464 helix: 0.61 (0.14), residues: 1649 sheet: -1.97 (0.24), residues: 388 loop : -2.22 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 796 TYR 0.026 0.001 TYR F 639 PHE 0.022 0.001 PHE C 605 TRP 0.020 0.001 TRP D 545 HIS 0.003 0.001 HIS C 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (27953) covalent geometry : angle 0.57525 / 0.28 (37809) hydrogen bonds : bond 0.03117 / 2.12 ( 1076) hydrogen bonds : angle 4.30501 / 3.07 ( 3099) Misc. bond : bond 0.00141 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6434 (p90) REVERT: B 181 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9169 (mp) REVERT: B 331 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8919 (tm-30) REVERT: B 412 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: B 427 GLU cc_start: 0.7671 (tt0) cc_final: 0.7164 (tm-30) REVERT: C 412 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: C 605 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8397 (p90) REVERT: C 629 ARG cc_start: 0.9272 (mtm110) cc_final: 0.9040 (mtm110) REVERT: D 404 MET cc_start: 0.8859 (mmm) cc_final: 0.8364 (tpp) REVERT: D 552 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.7953 (tmm-80) REVERT: E 257 GLU cc_start: 0.7661 (tt0) cc_final: 0.7295 (tm-30) REVERT: E 564 MET cc_start: 0.7675 (mmm) cc_final: 0.7430 (mmm) REVERT: E 604 MET cc_start: 0.8414 (ppp) cc_final: 0.7973 (ppp) REVERT: F 194 LEU cc_start: 0.8621 (tt) cc_final: 0.8233 (mt) REVERT: F 217 GLU cc_start: 0.8667 (pt0) cc_final: 0.8071 (tt0) REVERT: F 279 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7808 (tp30) REVERT: F 299 MET cc_start: 0.5200 (mpp) cc_final: 0.4822 (mpp) REVERT: F 319 GLU cc_start: 0.7768 (tp30) cc_final: 0.7169 (mm-30) REVERT: F 323 HIS cc_start: 0.7714 (m90) cc_final: 0.6343 (m-70) REVERT: F 377 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6291 (pp) REVERT: F 387 LEU cc_start: 0.7725 (mt) cc_final: 0.7204 (tp) REVERT: F 670 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7517 (mmt-90) REVERT: F 827 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.5586 (pt0) outliers start: 50 outliers final: 29 residues processed: 216 average time/residue: 0.1822 time to fit residues: 63.9435 Evaluate side-chains 209 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 822 MET Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 290 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 685 HIS C 812 GLN E 813 GLN E 829 HIS F 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081005 restraints weight = 51576.978| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.43 r_work: 0.2981 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27957 Z= 0.125 Angle : 0.588 15.660 37809 Z= 0.287 Chirality : 0.043 0.199 4328 Planarity : 0.004 0.083 4946 Dihedral : 7.774 120.910 4009 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.35 % Favored : 90.59 % Rotamer: Outliers : 1.92 % Allowed : 15.82 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.17 (0.15), residues: 3464 helix: 0.62 (0.14), residues: 1679 sheet: -1.86 (0.25), residues: 386 loop : -2.21 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 357 TYR 0.022 0.001 TYR F 639 PHE 0.027 0.001 PHE D 798 TRP 0.021 0.002 TRP D 545 HIS 0.007 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (27953) covalent geometry : angle 0.58776 / 0.29 (37809) hydrogen bonds : bond 0.03264 / 2.22 ( 1076) hydrogen bonds : angle 4.30013 / 3.06 ( 3099) Misc. bond : bond 0.00152 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 ILE cc_start: 0.9564 (OUTLIER) cc_final: 0.9170 (mp) REVERT: B 331 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8940 (tm-30) REVERT: B 412 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: B 427 GLU cc_start: 0.7698 (tt0) cc_final: 0.7224 (tm-30) REVERT: B 428 MET cc_start: 0.8673 (ttm) cc_final: 0.8380 (ppp) REVERT: B 603 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8129 (p90) REVERT: C 605 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (p90) REVERT: D 404 MET cc_start: 0.8857 (mmm) cc_final: 0.8365 (tpp) REVERT: D 552 ARG cc_start: 0.8523 (ttp-170) cc_final: 0.7988 (tmm-80) REVERT: D 648 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9092 (pp) REVERT: D 837 ASN cc_start: 0.8327 (m-40) cc_final: 0.7534 (p0) REVERT: E 245 MET cc_start: 0.5472 (mmt) cc_final: 0.4891 (mmp) REVERT: E 257 GLU cc_start: 0.7592 (tt0) cc_final: 0.7274 (tm-30) REVERT: E 564 MET cc_start: 0.7739 (mmm) cc_final: 0.7505 (mmm) REVERT: E 604 MET cc_start: 0.8432 (ppp) cc_final: 0.8017 (ppp) REVERT: F 194 LEU cc_start: 0.8662 (tt) cc_final: 0.8289 (mt) REVERT: F 217 GLU cc_start: 0.8653 (pt0) cc_final: 0.8038 (tt0) REVERT: F 299 MET cc_start: 0.5527 (mpp) cc_final: 0.5155 (mpp) REVERT: F 323 HIS cc_start: 0.7777 (m90) cc_final: 0.7346 (m-70) REVERT: F 377 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6324 (pp) REVERT: F 387 LEU cc_start: 0.7718 (mt) cc_final: 0.7203 (tp) REVERT: F 670 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7444 (mpt180) REVERT: F 827 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5523 (pt0) outliers start: 55 outliers final: 36 residues processed: 223 average time/residue: 0.1788 time to fit residues: 65.1049 Evaluate side-chains 212 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 311 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 813 GLN F 685 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.116695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.078272 restraints weight = 51950.479| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.41 r_work: 0.2921 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27957 Z= 0.225 Angle : 0.670 14.780 37809 Z= 0.330 Chirality : 0.046 0.182 4328 Planarity : 0.005 0.093 4946 Dihedral : 8.055 118.679 4009 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.45 % Favored : 89.46 % Rotamer: Outliers : 2.06 % Allowed : 16.31 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.34 (0.15), residues: 3464 helix: 0.46 (0.14), residues: 1677 sheet: -1.86 (0.25), residues: 385 loop : -2.29 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 222 TYR 0.026 0.002 TYR F 639 PHE 0.033 0.002 PHE C 605 TRP 0.024 0.002 TRP C 545 HIS 0.006 0.001 HIS C 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (27953) covalent geometry : angle 0.67039 / 0.33 (37809) hydrogen bonds : bond 0.04160 / 2.84 ( 1076) hydrogen bonds : angle 4.49202 / 3.19 ( 3099) Misc. bond : bond 0.00204 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 169 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 181 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9191 (mp) REVERT: B 331 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8972 (tm-30) REVERT: B 412 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: B 428 MET cc_start: 0.8670 (ttm) cc_final: 0.8089 (tmm) REVERT: B 554 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5770 (pt) REVERT: B 603 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8311 (p90) REVERT: B 623 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.5779 (p90) REVERT: C 605 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8388 (p90) REVERT: D 404 MET cc_start: 0.8913 (mmm) cc_final: 0.8347 (tpp) REVERT: D 648 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9073 (pp) REVERT: D 837 ASN cc_start: 0.8405 (m-40) cc_final: 0.7633 (p0) REVERT: E 257 GLU cc_start: 0.7603 (tt0) cc_final: 0.7273 (tm-30) REVERT: E 564 MET cc_start: 0.7729 (mmm) cc_final: 0.7429 (mmm) REVERT: E 813 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6423 (pp30) REVERT: E 822 MET cc_start: 0.5135 (ptm) cc_final: 0.4932 (ptp) REVERT: F 194 LEU cc_start: 0.8674 (tt) cc_final: 0.8250 (mt) REVERT: F 299 MET cc_start: 0.4749 (mpp) cc_final: 0.4497 (mpp) REVERT: F 323 HIS cc_start: 0.7759 (m90) cc_final: 0.7552 (m-70) REVERT: F 377 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6249 (pp) REVERT: F 387 LEU cc_start: 0.7720 (mt) cc_final: 0.7194 (tp) REVERT: F 670 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7509 (mmt-90) REVERT: F 827 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.5807 (pt0) outliers start: 59 outliers final: 34 residues processed: 220 average time/residue: 0.1700 time to fit residues: 61.4115 Evaluate side-chains 208 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 813 GLN Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 206 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 290 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.118778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080441 restraints weight = 51467.881| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.41 r_work: 0.2960 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27957 Z= 0.118 Angle : 0.602 14.986 37809 Z= 0.296 Chirality : 0.043 0.197 4328 Planarity : 0.004 0.084 4946 Dihedral : 7.829 116.938 4009 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.53 % Rotamer: Outliers : 1.54 % Allowed : 16.98 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3464 helix: 0.60 (0.14), residues: 1682 sheet: -1.78 (0.25), residues: 385 loop : -2.24 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.026 0.001 TYR F 639 PHE 0.025 0.001 PHE D 798 TRP 0.023 0.002 TRP E 545 HIS 0.004 0.001 HIS E 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (27953) covalent geometry : angle 0.60218 / 0.30 (37809) hydrogen bonds : bond 0.03368 / 2.29 ( 1076) hydrogen bonds : angle 4.41172 / 3.13 ( 3099) Misc. bond : bond 0.00150 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8615 (mmm-85) cc_final: 0.8330 (mmm160) REVERT: B 181 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9180 (mp) REVERT: B 331 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8965 (tm-30) REVERT: B 412 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: B 428 MET cc_start: 0.8657 (ttm) cc_final: 0.8067 (ppp) REVERT: B 603 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8334 (p90) REVERT: C 412 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: C 605 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8420 (p90) REVERT: C 629 ARG cc_start: 0.9260 (mtm110) cc_final: 0.9036 (mtm110) REVERT: D 404 MET cc_start: 0.8875 (mmm) cc_final: 0.8387 (tpp) REVERT: D 552 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8023 (tmm-80) REVERT: D 648 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9080 (pp) REVERT: E 257 GLU cc_start: 0.7565 (tt0) cc_final: 0.7246 (tm-30) REVERT: E 822 MET cc_start: 0.5215 (ptm) cc_final: 0.5013 (ptp) REVERT: F 194 LEU cc_start: 0.8681 (tt) cc_final: 0.8272 (mt) REVERT: F 217 GLU cc_start: 0.8679 (pt0) cc_final: 0.8030 (tt0) REVERT: F 279 GLU cc_start: 0.8258 (tp30) cc_final: 0.8055 (tp30) REVERT: F 299 MET cc_start: 0.5150 (mpp) cc_final: 0.4930 (mpp) REVERT: F 323 HIS cc_start: 0.7690 (m90) cc_final: 0.7400 (m-70) REVERT: F 377 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6238 (pp) REVERT: F 387 LEU cc_start: 0.7685 (mt) cc_final: 0.7191 (tp) REVERT: F 670 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7493 (mpt180) REVERT: F 827 GLN cc_start: 0.6481 (OUTLIER) cc_final: 0.5758 (pt0) outliers start: 44 outliers final: 29 residues processed: 210 average time/residue: 0.1867 time to fit residues: 63.7095 Evaluate side-chains 205 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 58 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 340 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS E 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.080987 restraints weight = 51485.739| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.45 r_work: 0.2984 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.003 0.042 27957 Z= 0.113 Angle : 0.592 16.334 37809 Z= 0.289 Chirality : 0.043 0.203 4328 Planarity : 0.004 0.084 4946 Dihedral : 7.643 114.983 4007 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.64 % Favored : 90.30 % Rotamer: Outliers : 1.47 % Allowed : 17.25 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.06 (0.15), residues: 3464 helix: 0.70 (0.14), residues: 1688 sheet: -1.66 (0.25), residues: 381 loop : -2.22 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 332 TYR 0.025 0.001 TYR F 639 PHE 0.027 0.001 PHE D 798 TRP 0.023 0.002 TRP E 545 HIS 0.009 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (27953) covalent geometry : angle 0.59157 / 0.29 (37809) hydrogen bonds : bond 0.03180 / 2.17 ( 1076) hydrogen bonds : angle 4.34255 / 3.09 ( 3099) Misc. bond : bond 0.00133 / 0.06 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8322 (mmm160) REVERT: B 181 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9169 (mp) REVERT: B 331 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8981 (tm-30) REVERT: B 412 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: B 428 MET cc_start: 0.8642 (ttm) cc_final: 0.8082 (tmm) REVERT: B 603 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8393 (p90) REVERT: C 412 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: C 605 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8393 (p90) REVERT: D 404 MET cc_start: 0.8870 (mmm) cc_final: 0.8375 (tpp) REVERT: D 552 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8039 (tmm-80) REVERT: D 648 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9074 (pp) REVERT: D 817 ASP cc_start: 0.8162 (m-30) cc_final: 0.7751 (m-30) REVERT: E 241 ASP cc_start: 0.6564 (OUTLIER) cc_final: 0.6081 (p0) REVERT: E 257 GLU cc_start: 0.7574 (tt0) cc_final: 0.7261 (tm-30) REVERT: E 822 MET cc_start: 0.5329 (ptm) cc_final: 0.5091 (ptp) REVERT: F 194 LEU cc_start: 0.8687 (tt) cc_final: 0.8261 (mt) REVERT: F 217 GLU cc_start: 0.8672 (pt0) cc_final: 0.8016 (tt0) REVERT: F 299 MET cc_start: 0.4992 (mpp) cc_final: 0.4774 (mpp) REVERT: F 319 GLU cc_start: 0.7841 (tp30) cc_final: 0.7601 (tp30) REVERT: F 323 HIS cc_start: 0.7794 (m90) cc_final: 0.7253 (m-70) REVERT: F 377 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6266 (pp) REVERT: F 387 LEU cc_start: 0.7632 (mt) cc_final: 0.7164 (tp) REVERT: F 595 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6682 (t70) REVERT: F 604 MET cc_start: 0.6369 (ttp) cc_final: 0.6110 (tmm) REVERT: F 670 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.7523 (mpt180) REVERT: F 827 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5331 (pt0) outliers start: 42 outliers final: 26 residues processed: 202 average time/residue: 0.1749 time to fit residues: 58.1359 Evaluate side-chains 200 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 412 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 688 VAL Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 595 ASP Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 751 LEU Chi-restraints excluded: chain F residue 827 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 293 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 HIS ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 813 GLN F 335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.116810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079099 restraints weight = 51594.744| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.71 r_work: 0.2919 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27957 Z= 0.211 Angle : 0.667 15.901 37809 Z= 0.327 Chirality : 0.046 0.192 4328 Planarity : 0.005 0.092 4946 Dihedral : 7.896 113.576 4007 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.16 % Favored : 89.75 % Rotamer: Outliers : 1.61 % Allowed : 17.22 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 3464 helix: 0.59 (0.13), residues: 1682 sheet: -1.73 (0.25), residues: 385 loop : -2.23 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 321 TYR 0.025 0.002 TYR F 639 PHE 0.033 0.002 PHE C 605 TRP 0.024 0.002 TRP E 545 HIS 0.007 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (27953) covalent geometry : angle 0.66676 / 0.33 (37809) hydrogen bonds : bond 0.04045 / 2.76 ( 1076) hydrogen bonds : angle 4.48620 / 3.19 ( 3099) Misc. bond : bond 0.00196 / 0.09 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7302.93 seconds wall clock time: 125 minutes 22.23 seconds (7522.23 seconds total)