Starting phenix.real_space_refine on Mon Sep 14 13:17:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553.map" model { file = "/net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w6e_21553/09_2026/6w6e_21553_neut.cif" } resolution = 3.7 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= 0.002 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 74 5.16 5 C 19113 2.51 5 N 5603 2.21 5 O 5981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30805 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5222 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 13 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: 4219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4219 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 24, 'TRANS': 521} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2694 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 12, 'TRANS': 344} 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: 6.99, per 1000 atoms: 0.23 Number of scatterers: 30805 At special positions: 0 Unit cell: (112.77, 142.842, 241.65, 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 74 16.00 P 34 15.00 O 5981 8.00 N 5603 7.00 C 19113 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7262 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 36 sheets defined 52.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.571A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.620A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 4.104A pdb=" N VAL A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.736A pdb=" N ARG A 233 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.897A pdb=" N SER A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.753A pdb=" N TYR A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 removed outlier: 3.892A pdb=" N GLU A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 362 removed outlier: 5.352A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 3.874A pdb=" N LEU A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 391 through 407 removed outlier: 3.823A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 removed outlier: 3.541A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 494 removed outlier: 3.692A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 467 " --> pdb=" O TRP A 463 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 4.000A pdb=" N GLU A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 518 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.909A pdb=" N LYS A 560 " --> pdb=" O GLY A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 575 through 584 removed outlier: 3.842A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.691A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 4.121A pdb=" N MET A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 4.012A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.623A pdb=" N VAL A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.514A pdb=" N ALA A 684 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.835A pdb=" N LEU A 692 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.581A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 761 through 776 removed outlier: 3.780A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 797 removed outlier: 4.230A pdb=" N GLY A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.819A pdb=" N ARG A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.511A 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 removed outlier: 3.520A pdb=" N GLU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.607A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.503A pdb=" N MET B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.787A pdb=" N SER B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.962A pdb=" N VAL B 284 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 285 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.809A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 removed outlier: 4.305A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 343 through 362 removed outlier: 3.935A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 377 removed outlier: 3.796A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.620A pdb=" N ASP B 393 " --> pdb=" O ASP B 389 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 removed outlier: 4.455A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 468 removed outlier: 3.578A pdb=" N LYS B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 563 removed outlier: 3.590A pdb=" N LYS B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.777A pdb=" N LYS B 570 " --> pdb=" O GLU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.977A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.995A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 3.939A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 3.647A pdb=" N VAL B 645 " --> pdb=" O LYS B 642 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 646 " --> pdb=" O HIS B 643 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 647 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.516A pdb=" N VAL B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.607A pdb=" N LYS B 683 " --> pdb=" O GLU B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 693 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 758 through 760 No H-bonds generated for 'chain 'B' and resid 758 through 760' Processing helix chain 'B' and resid 761 through 776 removed outlier: 3.583A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 786 through 796 removed outlier: 4.189A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 824 removed outlier: 3.573A pdb=" N ARG B 809 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.703A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.503A pdb=" N LEU C 232 " --> pdb=" O PRO C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 306 removed outlier: 3.968A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG C 306 " --> pdb=" O PRO C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.577A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.704A 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: 4.157A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 407 removed outlier: 3.528A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 432 removed outlier: 3.692A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS C 432 " --> pdb=" O MET C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 469 removed outlier: 4.216A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 557 through 569 removed outlier: 5.136A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 591 removed outlier: 4.154A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 626 Processing helix chain 'C' and resid 627 through 631 removed outlier: 3.834A pdb=" N MET C 631 " --> pdb=" O GLU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 3.568A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 680 through 684 removed outlier: 3.633A pdb=" N ALA C 684 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 Processing helix chain 'C' and resid 691 through 698 removed outlier: 4.354A pdb=" N VAL C 695 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 739 removed outlier: 4.458A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.722A pdb=" N ILE C 744 " --> pdb=" O LYS C 740 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 745 " --> pdb=" O PRO C 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 745' Processing helix chain 'C' and resid 760 through 777 removed outlier: 3.687A 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: 3.787A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 824 removed outlier: 3.819A pdb=" N ARG C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.670A pdb=" N ILE D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 226 Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.824A pdb=" N ARG D 233 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.640A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 343 through 362 removed outlier: 5.087A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 381 removed outlier: 4.244A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 407 removed outlier: 4.278A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 563 Processing helix chain 'D' and resid 564 through 570 removed outlier: 3.576A pdb=" N LYS D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 592 removed outlier: 3.775A pdb=" N VAL D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 626 Processing helix chain 'D' and resid 642 through 649 removed outlier: 3.593A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 670 removed outlier: 3.785A pdb=" N ARG D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 690 Processing helix chain 'D' and resid 691 through 696 Processing helix chain 'D' and resid 727 through 739 removed outlier: 4.230A pdb=" N ALA D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 734 " --> pdb=" O GLN D 730 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG D 736 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 745 Processing helix chain 'D' and resid 760 through 776 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 824 removed outlier: 3.579A pdb=" N LEU D 824 " --> pdb=" O ALA D 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 removed outlier: 4.201A pdb=" N ILE E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 241 through 245 removed outlier: 3.644A pdb=" N SER E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 270 removed outlier: 3.877A pdb=" N ALA E 270 " --> pdb=" O ILE E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 283 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 316 through 324 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 343 through 354 Processing helix chain 'E' and resid 355 through 362 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 386 through 405 removed outlier: 4.108A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 547 removed outlier: 4.695A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 575 through 590 removed outlier: 3.544A pdb=" N ARG E 590 " --> pdb=" O VAL E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 626 removed outlier: 3.863A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 649 removed outlier: 3.850A pdb=" N VAL E 645 " --> pdb=" O LYS E 642 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 649 " --> pdb=" O ALA E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 696 removed outlier: 3.800A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 739 removed outlier: 4.098A pdb=" N ALA E 733 " --> pdb=" O GLU E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 742 through 747 removed outlier: 3.514A pdb=" N ARG E 746 " --> pdb=" O PHE E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 786 through 798 removed outlier: 4.080A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 820 removed outlier: 3.701A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 826 Processing helix chain 'F' and resid 169 through 175 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 269 removed outlier: 3.910A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 306 removed outlier: 3.904A pdb=" N MET F 303 " --> pdb=" O MET F 299 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 324 Processing helix chain 'F' and resid 343 through 355 removed outlier: 4.190A pdb=" N GLY F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 359 Processing helix chain 'F' and resid 367 through 377 Processing helix chain 'F' and resid 386 through 406 removed outlier: 3.874A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 544 Processing helix chain 'F' and resid 556 through 563 removed outlier: 3.918A pdb=" N LYS F 560 " --> pdb=" O GLY F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 569 Processing helix chain 'F' and resid 575 through 591 removed outlier: 4.005A pdb=" N VAL F 586 " --> pdb=" O VAL F 582 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F 588 " --> pdb=" O ASP F 584 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 591 " --> pdb=" O ARG F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 626 removed outlier: 3.566A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 648 removed outlier: 3.844A pdb=" N THR F 644 " --> pdb=" O GLU F 641 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 670 removed outlier: 4.120A pdb=" N ARG F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 687 through 696 Processing helix chain 'F' and resid 728 through 739 removed outlier: 3.634A pdb=" N PHE F 739 " --> pdb=" O VAL F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 776 removed outlier: 3.875A pdb=" N ILE F 764 " --> pdb=" O GLU F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 786 through 797 Processing helix chain 'F' and resid 804 through 815 Processing helix chain 'F' and resid 815 through 824 removed outlier: 3.762A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 59 removed outlier: 4.478A pdb=" N VAL I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 88 through 108 removed outlier: 3.553A pdb=" N ILE I 95 " --> pdb=" O ILE I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 137 Processing helix chain 'I' and resid 147 through 155 removed outlier: 3.539A pdb=" N TYR I 155 " --> pdb=" O ALA I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 221 Processing helix chain 'I' and resid 223 through 226 Processing helix chain 'I' and resid 227 through 245 Processing helix chain 'I' and resid 275 through 287 removed outlier: 5.099A pdb=" N ASP I 284 " --> pdb=" O ARG I 280 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU I 285 " --> pdb=" O ILE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 301 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 314 through 318 Processing helix chain 'I' and resid 319 through 330 Processing helix chain 'I' and resid 343 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 3.520A pdb=" N THR A 166 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP A 278 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 314 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 7.918A 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 633 through 635 removed outlier: 3.580A pdb=" N ASP A 679 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 603 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N LEU A 751 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 604 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702 removed outlier: 3.683A pdb=" N LEU A 701 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 784 Processing sheet with id=AA6, first strand: chain 'A' and resid 837 through 838 removed outlier: 3.634A pdb=" N ASN A 837 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 167 removed outlier: 7.003A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ARG B 310 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 315 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 206 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 633 through 635 removed outlier: 7.142A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.583A pdb=" N LEU B 701 " --> pdb=" O VAL B 709 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 782 through 785 removed outlier: 7.611A pdb=" N GLN B 782 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N VAL B 836 " --> pdb=" O GLN B 782 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLN B 784 " --> pdb=" O VAL B 836 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N VAL B 838 " --> pdb=" O GLN B 784 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 837 " --> pdb=" O SER B 844 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 238 through 239 removed outlier: 6.458A pdb=" N VAL C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP C 278 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 275 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ALA C 314 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE C 277 " --> pdb=" O ALA C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.454A pdb=" N ARG C 365 " --> pdb=" O VAL C 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 602 through 603 Processing sheet with id=AB5, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.507A pdb=" N ASP C 679 " --> pdb=" O ILE C 634 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 700 through 702 removed outlier: 3.763A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 783 through 785 removed outlier: 6.446A pdb=" N GLN C 784 " --> pdb=" O VAL C 836 " (cutoff:3.500A) removed outlier: 8.299A 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: 3.622A pdb=" N THR D 166 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 239 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 313 through 315 removed outlier: 8.167A pdb=" N THR D 315 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU D 204 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.802A pdb=" N ARG D 365 " --> pdb=" O VAL D 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 602 through 603 removed outlier: 7.119A pdb=" N PHE D 603 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE D 634 " --> pdb=" O ASP D 679 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 700 through 701 removed outlier: 3.643A pdb=" N LEU D 701 " --> pdb=" O VAL D 709 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 782 through 784 Processing sheet with id=AC5, first strand: chain 'E' and resid 277 through 278 removed outlier: 7.205A pdb=" N ILE E 277 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR E 315 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU E 204 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 602 through 603 removed outlier: 3.778A pdb=" N PHE E 603 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL E 676 " --> pdb=" O ILE E 717 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 632 " --> pdb=" O LEU E 677 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASP E 679 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE E 634 " --> pdb=" O ASP E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 700 through 702 Processing sheet with id=AC8, first strand: chain 'F' and resid 238 through 239 removed outlier: 6.707A pdb=" N VAL F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP F 278 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 632 through 635 removed outlier: 6.495A pdb=" N GLY F 601 " --> pdb=" O LEU F 716 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU F 718 " --> pdb=" O GLY F 601 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE F 603 " --> pdb=" O LEU F 718 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 700 through 702 removed outlier: 3.638A pdb=" N LEU F 701 " --> pdb=" O VAL F 709 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 709 " --> pdb=" O LEU F 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 783 through 784 Processing sheet with id=AD3, first strand: chain 'F' and resid 837 through 838 Processing sheet with id=AD4, first strand: chain 'I' and resid 23 through 27 removed outlier: 4.799A pdb=" N VAL I 16 " --> pdb=" O VAL I 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 23 through 27 removed outlier: 4.799A pdb=" N VAL I 16 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL I 5 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA I 114 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE I 144 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 116 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN I 146 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR I 118 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AD7, first strand: chain 'I' and resid 78 through 81 Processing sheet with id=AD8, first strand: chain 'I' and resid 187 through 196 removed outlier: 5.378A pdb=" N VAL I 188 " --> pdb=" O GLY I 184 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLY I 184 " --> pdb=" O VAL I 188 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL I 190 " --> pdb=" O GLU I 182 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU I 182 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 250 through 255 1283 hydrogen bonds defined for protein. 3642 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: 5.55 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 10714 1.35 - 1.50: 7212 1.50 - 1.65: 13155 1.65 - 1.80: 90 1.80 - 1.95: 48 Bond restraints: 31219 Sorted by residual: bond pdb=" CA VAL I 115 " pdb=" C VAL I 115 " ideal model delta sigma weight residual 1.522 1.349 0.173 1.21e-02 6.83e+03 2.04e+02 bond pdb=" CA VAL A 473 " pdb=" C VAL A 473 " ideal model delta sigma weight residual 1.523 1.406 0.117 1.27e-02 6.20e+03 8.53e+01 bond pdb=" CA LEU I 167 " pdb=" C LEU I 167 " ideal model delta sigma weight residual 1.523 1.410 0.113 1.23e-02 6.61e+03 8.45e+01 bond pdb=" CA ILE I 95 " pdb=" C ILE I 95 " ideal model delta sigma weight residual 1.524 1.412 0.112 1.23e-02 6.61e+03 8.35e+01 bond pdb=" N ASP I 8 " pdb=" CA ASP I 8 " ideal model delta sigma weight residual 1.463 1.348 0.114 1.28e-02 6.10e+03 7.98e+01 ... (remaining 31214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 41279 2.66 - 5.31: 796 5.31 - 7.97: 117 7.97 - 10.63: 20 10.63 - 13.28: 20 Bond angle restraints: 42232 Sorted by residual: angle pdb=" C MET I 319 " pdb=" N PRO I 320 " pdb=" CA PRO I 320 " ideal model delta sigma weight residual 119.56 128.64 -9.08 1.01e+00 9.80e-01 8.07e+01 angle pdb=" N ILE B 413 " pdb=" CA ILE B 413 " pdb=" C ILE B 413 " ideal model delta sigma weight residual 113.47 104.85 8.62 1.01e+00 9.80e-01 7.28e+01 angle pdb=" C ASN I 340 " pdb=" N PRO I 341 " pdb=" CA PRO I 341 " ideal model delta sigma weight residual 119.47 128.84 -9.37 1.16e+00 7.43e-01 6.52e+01 angle pdb=" C LEU I 255 " pdb=" N PRO I 256 " pdb=" CA PRO I 256 " ideal model delta sigma weight residual 119.85 127.13 -7.28 1.01e+00 9.80e-01 5.20e+01 angle pdb=" C GLU I 334 " pdb=" N PRO I 335 " pdb=" CA PRO I 335 " ideal model delta sigma weight residual 119.76 126.17 -6.41 1.00e+00 1.00e+00 4.11e+01 ... (remaining 42227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.13: 18900 35.13 - 70.26: 428 70.26 - 105.39: 93 105.39 - 140.52: 14 140.52 - 175.66: 15 Dihedral angle restraints: 19450 sinusoidal: 8182 harmonic: 11268 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 -118.04 -61.96 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.57 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" CA LYS I 333 " pdb=" C LYS I 333 " pdb=" N GLU I 334 " pdb=" CA GLU I 334 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 19447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3837 0.060 - 0.119: 835 0.119 - 0.179: 111 0.179 - 0.239: 21 0.239 - 0.298: 18 Chirality restraints: 4822 Sorted by residual: chirality pdb=" C3' AGS A 901 " pdb=" C2' AGS A 901 " pdb=" C4' AGS A 901 " pdb=" O3' AGS A 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.67 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ALA I 349 " pdb=" N ALA I 349 " pdb=" C ALA I 349 " pdb=" CB ALA I 349 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' AGS B 901 " pdb=" C2' AGS B 901 " pdb=" C4' AGS B 901 " pdb=" O3' AGS B 901 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4819 not shown) Planarity restraints: 5533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS I 333 " 0.069 2.00e-02 2.50e+03 1.44e-01 2.08e+02 pdb=" C LYS I 333 " -0.249 2.00e-02 2.50e+03 pdb=" O LYS I 333 " 0.097 2.00e-02 2.50e+03 pdb=" N GLU I 334 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 491 " 0.025 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C GLU A 491 " -0.088 2.00e-02 2.50e+03 pdb=" O GLU A 491 " 0.033 2.00e-02 2.50e+03 pdb=" N ARG A 492 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 500 " 0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C ALA A 500 " -0.078 2.00e-02 2.50e+03 pdb=" O ALA A 500 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU A 501 " 0.027 2.00e-02 2.50e+03 ... (remaining 5530 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 6 1.83 - 2.60: 403 2.60 - 3.37: 40850 3.37 - 4.13: 67966 4.13 - 4.90: 125908 Nonbonded interactions: 235133 Sorted by model distance: nonbonded pdb=" CZ ARG A 462 " pdb=" CE MET A 528 " model vdw 1.067 3.690 nonbonded pdb=" NH2 ARG A 462 " pdb=" CE MET A 528 " model vdw 1.111 3.540 nonbonded pdb=" NH1 ARG A 462 " pdb=" SD MET A 528 " model vdw 1.424 3.480 nonbonded pdb=" NH1 ARG A 462 " pdb=" CE MET A 528 " model vdw 1.447 3.540 nonbonded pdb=" O ARG A 462 " pdb=" OE1 GLU A 466 " model vdw 1.510 3.040 ... (remaining 235128 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 469 or resid 530 through 901)) selection = (chain 'B' and (resid 159 through 288 or resid 296 through 901)) selection = (chain 'C' and (resid 159 through 288 or resid 296 through 901)) } ncs_group { reference = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 901)) selection = (chain 'F' and (resid 159 through 407 or resid 530 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.860 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 0.173 31223 Z= 0.605 Angle : 0.960 13.282 42232 Z= 0.554 Chirality : 0.053 0.298 4822 Planarity : 0.006 0.144 5533 Dihedral : 17.484 175.655 12188 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.64 % Favored : 89.15 % Rotamer: Outliers : 0.53 % Allowed : 5.99 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.11), residues: 3890 helix: -1.98 (0.10), residues: 1885 sheet: -3.32 (0.21), residues: 395 loop : -3.21 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 809 TYR 0.011 0.001 TYR D 164 PHE 0.012 0.001 PHE A 753 TRP 0.029 0.001 TRP D 545 HIS 0.010 0.001 HIS E 829 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.60 (31219) covalent geometry : angle 0.95998 / 0.55 (42232) hydrogen bonds : bond 0.16331 / 11.17 ( 1278) hydrogen bonds : angle 6.49378 / 4.57 ( 3642) Misc. bond : bond 0.00203 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 397 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7247 (p0) cc_final: 0.6896 (p0) REVERT: B 636 MET cc_start: 0.8514 (mmm) cc_final: 0.8088 (mmm) REVERT: B 822 MET cc_start: 0.7943 (mtp) cc_final: 0.7436 (mtp) REVERT: D 257 GLU cc_start: 0.7252 (pt0) cc_final: 0.6553 (pt0) REVERT: D 631 MET cc_start: 0.8433 (ptt) cc_final: 0.8226 (ptt) REVERT: E 245 MET cc_start: 0.6174 (mmt) cc_final: 0.5821 (mmt) REVERT: E 281 HIS cc_start: 0.6790 (p90) cc_final: 0.6568 (p-80) REVERT: E 404 MET cc_start: 0.8058 (mmm) cc_final: 0.7402 (ptm) REVERT: E 636 MET cc_start: 0.8382 (mmp) cc_final: 0.8113 (mmp) REVERT: F 304 LEU cc_start: 0.8544 (tp) cc_final: 0.7980 (pp) REVERT: F 324 ILE cc_start: 0.7895 (pt) cc_final: 0.7643 (mt) outliers start: 17 outliers final: 13 residues processed: 413 average time/residue: 0.2534 time to fit residues: 152.1857 Evaluate side-chains 175 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 674 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain F residue 738 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 ASN A 323 HIS A 361 HIS A 705 HIS A 784 GLN B 221 GLN B 361 HIS B 663 GLN B 705 HIS B 812 GLN C 221 GLN C 323 HIS C 643 HIS C 663 GLN C 685 HIS C 730 GLN C 818 GLN D 298 ASN D 643 HIS D 685 HIS ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 272 GLN E 323 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN E 818 GLN E 829 HIS F 268 ASN F 685 HIS I 254 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.065897 restraints weight = 102089.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067299 restraints weight = 56192.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068266 restraints weight = 37674.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068835 restraints weight = 29213.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069104 restraints weight = 25153.012| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31223 Z= 0.148 Angle : 0.684 12.075 42232 Z= 0.339 Chirality : 0.044 0.220 4822 Planarity : 0.005 0.082 5533 Dihedral : 15.801 177.619 4770 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.48 % Favored : 91.44 % Rotamer: Outliers : 1.34 % Allowed : 11.92 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -2.48 (0.13), residues: 3890 helix: -0.60 (0.12), residues: 1894 sheet: -2.84 (0.22), residues: 425 loop : -2.54 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 590 TYR 0.018 0.001 TYR D 802 PHE 0.030 0.002 PHE D 798 TRP 0.021 0.001 TRP D 545 HIS 0.009 0.001 HIS E 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (31219) covalent geometry : angle 0.68439 / 0.34 (42232) hydrogen bonds : bond 0.04144 / 2.83 ( 1278) hydrogen bonds : angle 5.00861 / 3.56 ( 3642) Misc. bond : bond 0.00181 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7977 (tmm-80) REVERT: B 636 MET cc_start: 0.8840 (mmm) cc_final: 0.8328 (mmm) REVERT: D 338 TYR cc_start: 0.8513 (t80) cc_final: 0.8286 (t80) REVERT: D 631 MET cc_start: 0.8916 (ptt) cc_final: 0.8689 (ptt) REVERT: E 404 MET cc_start: 0.8188 (mmm) cc_final: 0.7337 (ptm) REVERT: F 304 LEU cc_start: 0.8450 (tp) cc_final: 0.8106 (pp) REVERT: F 324 ILE cc_start: 0.7841 (pt) cc_final: 0.7433 (tp) REVERT: F 679 ASP cc_start: 0.7742 (t0) cc_final: 0.7247 (t0) outliers start: 43 outliers final: 21 residues processed: 218 average time/residue: 0.1865 time to fit residues: 66.4107 Evaluate side-chains 158 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 823 LEU Chi-restraints excluded: chain F residue 833 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 221 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 379 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 198 optimal weight: 0.0670 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 GLN C 335 GLN C 361 HIS D 827 GLN E 323 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 685 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 768 GLN F 829 HIS I 294 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.064170 restraints weight = 102110.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.065600 restraints weight = 56514.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.066547 restraints weight = 37979.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067144 restraints weight = 29532.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067506 restraints weight = 25349.777| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31223 Z= 0.168 Angle : 0.655 10.744 42232 Z= 0.323 Chirality : 0.044 0.273 4822 Planarity : 0.005 0.086 5533 Dihedral : 14.277 172.891 4759 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.87 % Favored : 91.03 % Rotamer: Outliers : 2.03 % Allowed : 13.26 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.87 (0.14), residues: 3890 helix: -0.11 (0.12), residues: 1913 sheet: -2.62 (0.21), residues: 451 loop : -2.20 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 280 TYR 0.021 0.001 TYR D 802 PHE 0.027 0.002 PHE B 605 TRP 0.018 0.001 TRP D 545 HIS 0.006 0.001 HIS E 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (31219) covalent geometry : angle 0.65461 / 0.32 (42232) hydrogen bonds : bond 0.04016 / 2.74 ( 1278) hydrogen bonds : angle 4.73879 / 3.37 ( 3642) Misc. bond : bond 0.00175 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 603 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7147 (p90) REVERT: B 636 MET cc_start: 0.8968 (mmm) cc_final: 0.8339 (mmm) REVERT: D 251 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: D 311 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9190 (tt) REVERT: D 631 MET cc_start: 0.8969 (ptt) cc_final: 0.8731 (ptt) REVERT: D 718 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8850 (pt) REVERT: D 747 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9357 (pp) REVERT: E 404 MET cc_start: 0.8178 (mmm) cc_final: 0.7435 (ptm) REVERT: F 304 LEU cc_start: 0.8458 (tp) cc_final: 0.8041 (pp) REVERT: F 322 LYS cc_start: 0.7405 (tttt) cc_final: 0.7163 (mttp) REVERT: F 324 ILE cc_start: 0.7921 (pt) cc_final: 0.7478 (tp) REVERT: F 679 ASP cc_start: 0.7668 (t0) cc_final: 0.7125 (t0) REVERT: F 827 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: I 73 MET cc_start: -0.0101 (mtp) cc_final: -0.0372 (ptp) outliers start: 65 outliers final: 25 residues processed: 214 average time/residue: 0.1889 time to fit residues: 65.2262 Evaluate side-chains 163 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 266 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 383 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN E 323 HIS ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.095856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064993 restraints weight = 101452.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066397 restraints weight = 56295.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067327 restraints weight = 37902.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067930 restraints weight = 29577.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068199 restraints weight = 25414.739| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31223 Z= 0.134 Angle : 0.601 11.245 42232 Z= 0.297 Chirality : 0.043 0.214 4822 Planarity : 0.004 0.083 5533 Dihedral : 13.774 176.484 4759 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 1.97 % Allowed : 14.38 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.43 (0.14), residues: 3890 helix: 0.23 (0.13), residues: 1913 sheet: -2.30 (0.22), residues: 441 loop : -1.99 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 700 TYR 0.019 0.001 TYR E 164 PHE 0.020 0.001 PHE B 605 TRP 0.017 0.001 TRP D 545 HIS 0.005 0.001 HIS E 685 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (31219) covalent geometry : angle 0.60112 / 0.30 (42232) hydrogen bonds : bond 0.03439 / 2.35 ( 1278) hydrogen bonds : angle 4.50758 / 3.20 ( 3642) Misc. bond : bond 0.00161 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 ARG cc_start: 0.8258 (ptp90) cc_final: 0.8014 (ptp90) REVERT: B 331 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8700 (tm-30) REVERT: B 441 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.7974 (mtm110) REVERT: B 603 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7170 (p90) REVERT: C 575 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7031 (mp-120) REVERT: D 217 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: D 631 MET cc_start: 0.8918 (ptt) cc_final: 0.8673 (ptt) REVERT: D 822 MET cc_start: 0.8422 (ttm) cc_final: 0.8034 (ttm) REVERT: E 604 MET cc_start: 0.7996 (ppp) cc_final: 0.7711 (ppp) REVERT: F 304 LEU cc_start: 0.8540 (tp) cc_final: 0.8254 (pp) REVERT: F 322 LYS cc_start: 0.7416 (tttt) cc_final: 0.7183 (mttp) REVERT: F 324 ILE cc_start: 0.7946 (pt) cc_final: 0.7425 (tp) REVERT: F 679 ASP cc_start: 0.7627 (t0) cc_final: 0.7332 (t0) REVERT: F 827 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: I 73 MET cc_start: 0.0052 (mtp) cc_final: -0.0219 (ptp) outliers start: 63 outliers final: 28 residues processed: 207 average time/residue: 0.1825 time to fit residues: 62.7244 Evaluate side-chains 165 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 190 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 295 optimal weight: 0.0770 chunk 7 optimal weight: 7.9990 chunk 268 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 0.3980 chunk 50 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS E 362 HIS F 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.096639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065843 restraints weight = 101544.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067335 restraints weight = 55306.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068300 restraints weight = 36665.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.068906 restraints weight = 28361.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069170 restraints weight = 24307.840| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 31223 Z= 0.108 Angle : 0.582 12.423 42232 Z= 0.286 Chirality : 0.042 0.216 4822 Planarity : 0.004 0.080 5533 Dihedral : 13.531 177.791 4759 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 2.28 % Allowed : 14.78 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % 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: -1.09 (0.14), residues: 3890 helix: 0.50 (0.13), residues: 1911 sheet: -2.15 (0.22), residues: 452 loop : -1.80 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 736 TYR 0.014 0.001 TYR D 251 PHE 0.017 0.001 PHE B 605 TRP 0.016 0.001 TRP D 545 HIS 0.005 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (31219) covalent geometry : angle 0.58167 / 0.29 (42232) hydrogen bonds : bond 0.03181 / 2.16 ( 1278) hydrogen bonds : angle 4.34269 / 3.08 ( 3642) Misc. bond : bond 0.00146 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 156 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ASN cc_start: 0.8765 (m-40) cc_final: 0.8372 (m-40) REVERT: A 383 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9018 (t) REVERT: A 409 ARG cc_start: 0.8204 (ptp90) cc_final: 0.7990 (ptp90) REVERT: A 511 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: B 298 ASN cc_start: 0.8039 (t0) cc_final: 0.7822 (t0) REVERT: B 331 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8698 (tm-30) REVERT: B 441 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.7994 (mtm110) REVERT: B 603 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.7122 (p90) REVERT: B 636 MET cc_start: 0.9051 (mmm) cc_final: 0.8801 (mmt) REVERT: D 217 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: D 251 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: D 311 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9107 (tt) REVERT: D 631 MET cc_start: 0.8906 (ptt) cc_final: 0.8685 (ptt) REVERT: D 718 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8794 (pt) REVERT: E 603 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7269 (p90) REVERT: E 636 MET cc_start: 0.8716 (mmp) cc_final: 0.8339 (mmp) REVERT: F 207 GLU cc_start: 0.7802 (mp0) cc_final: 0.7553 (mm-30) REVERT: F 267 LYS cc_start: 0.9084 (tptt) cc_final: 0.8865 (ptmt) REVERT: F 304 LEU cc_start: 0.8550 (tp) cc_final: 0.8277 (pp) REVERT: F 324 ILE cc_start: 0.7838 (pt) cc_final: 0.7201 (tp) REVERT: F 827 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: I 73 MET cc_start: 0.0134 (mtp) cc_final: -0.0073 (ptp) outliers start: 73 outliers final: 26 residues processed: 221 average time/residue: 0.1872 time to fit residues: 67.7443 Evaluate side-chains 169 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 511 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 154 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.095428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064622 restraints weight = 101482.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.066042 restraints weight = 55722.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066991 restraints weight = 37317.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.067591 restraints weight = 29006.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067954 restraints weight = 24930.092| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31223 Z= 0.139 Angle : 0.601 12.584 42232 Z= 0.295 Chirality : 0.043 0.285 4822 Planarity : 0.004 0.084 5533 Dihedral : 13.453 178.553 4757 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.41 % Rotamer: Outliers : 2.03 % Allowed : 15.85 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3890 helix: 0.63 (0.13), residues: 1911 sheet: -2.04 (0.23), residues: 452 loop : -1.75 (0.17), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 332 TYR 0.013 0.001 TYR F 381 PHE 0.021 0.001 PHE B 605 TRP 0.013 0.001 TRP D 545 HIS 0.005 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (31219) covalent geometry : angle 0.60087 / 0.29 (42232) hydrogen bonds : bond 0.03348 / 2.27 ( 1278) hydrogen bonds : angle 4.34003 / 3.08 ( 3642) Misc. bond : bond 0.00149 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.9050 (t) REVERT: A 409 ARG cc_start: 0.8224 (ptp90) cc_final: 0.7999 (ptp90) REVERT: B 331 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8716 (tm-30) REVERT: B 441 ARG cc_start: 0.8706 (mtm-85) cc_final: 0.8111 (mtm110) REVERT: B 455 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8349 (ttpp) REVERT: B 603 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.7169 (p90) REVERT: B 636 MET cc_start: 0.9053 (mmm) cc_final: 0.8523 (mmt) REVERT: C 422 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7818 (mtp85) REVERT: D 217 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8178 (mm-30) REVERT: D 251 TYR cc_start: 0.7939 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: D 631 MET cc_start: 0.8924 (ptt) cc_final: 0.8698 (ptt) REVERT: D 718 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8836 (pt) REVERT: D 845 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8075 (tp) REVERT: E 603 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7242 (p90) REVERT: E 636 MET cc_start: 0.8754 (mmp) cc_final: 0.8354 (mmp) REVERT: F 207 GLU cc_start: 0.7844 (mp0) cc_final: 0.7607 (mm-30) REVERT: F 304 LEU cc_start: 0.8526 (tp) cc_final: 0.8210 (pp) REVERT: F 324 ILE cc_start: 0.7671 (pt) cc_final: 0.7075 (tp) REVERT: F 679 ASP cc_start: 0.7430 (t0) cc_final: 0.7204 (t0) REVERT: F 827 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6342 (pm20) REVERT: I 73 MET cc_start: 0.0258 (mtp) cc_final: 0.0041 (ptp) REVERT: I 229 MET cc_start: 0.2708 (ttt) cc_final: 0.2371 (mmm) outliers start: 65 outliers final: 40 residues processed: 199 average time/residue: 0.1815 time to fit residues: 59.8028 Evaluate side-chains 177 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 10 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 281 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 342 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.094264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063499 restraints weight = 101325.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.064888 restraints weight = 55545.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.065824 restraints weight = 37317.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066385 restraints weight = 29049.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066771 restraints weight = 25044.556| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31223 Z= 0.185 Angle : 0.635 12.774 42232 Z= 0.311 Chirality : 0.044 0.258 4822 Planarity : 0.004 0.088 5533 Dihedral : 13.460 178.591 4757 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.79 % Favored : 91.13 % Rotamer: Outliers : 2.12 % Allowed : 16.31 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.14), residues: 3890 helix: 0.68 (0.13), residues: 1910 sheet: -2.09 (0.23), residues: 448 loop : -1.79 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 409 TYR 0.012 0.001 TYR D 251 PHE 0.022 0.002 PHE B 605 TRP 0.012 0.001 TRP C 545 HIS 0.007 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (31219) covalent geometry : angle 0.63487 / 0.31 (42232) hydrogen bonds : bond 0.03666 / 2.50 ( 1278) hydrogen bonds : angle 4.45369 / 3.17 ( 3642) Misc. bond : bond 0.00157 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9083 (t) REVERT: B 331 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8744 (tm-30) REVERT: B 441 ARG cc_start: 0.8713 (mtm-85) cc_final: 0.8134 (mtm110) REVERT: B 603 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.7294 (p90) REVERT: B 605 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8505 (p90) REVERT: B 636 MET cc_start: 0.9071 (mmm) cc_final: 0.8611 (mmm) REVERT: C 422 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7667 (mtp85) REVERT: D 217 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: D 631 MET cc_start: 0.8921 (ptt) cc_final: 0.8704 (ptt) REVERT: D 718 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8881 (pt) REVERT: E 603 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7243 (p90) REVERT: E 636 MET cc_start: 0.8787 (mmp) cc_final: 0.8362 (mmp) REVERT: F 207 GLU cc_start: 0.7913 (mp0) cc_final: 0.7684 (mm-30) REVERT: F 304 LEU cc_start: 0.8658 (tp) cc_final: 0.8328 (pp) REVERT: F 324 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7072 (tp) REVERT: F 679 ASP cc_start: 0.7535 (t0) cc_final: 0.7193 (t0) REVERT: F 827 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6324 (pm20) outliers start: 68 outliers final: 43 residues processed: 195 average time/residue: 0.1872 time to fit residues: 60.8752 Evaluate side-chains 178 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 701 LEU Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 827 GLN Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 79 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 376 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 chunk 293 optimal weight: 8.9990 chunk 323 optimal weight: 0.2980 chunk 311 optimal weight: 10.0000 chunk 389 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 201 ASN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.095899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.065354 restraints weight = 101379.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.066834 restraints weight = 54895.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067786 restraints weight = 36547.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068366 restraints weight = 28203.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068742 restraints weight = 24187.520| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31223 Z= 0.110 Angle : 0.585 12.615 42232 Z= 0.286 Chirality : 0.042 0.227 4822 Planarity : 0.004 0.080 5533 Dihedral : 13.333 178.010 4756 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 1.97 % Allowed : 16.75 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3890 helix: 0.77 (0.13), residues: 1936 sheet: -1.91 (0.23), residues: 447 loop : -1.73 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 252 TYR 0.007 0.001 TYR D 655 PHE 0.023 0.001 PHE D 623 TRP 0.015 0.001 TRP D 545 HIS 0.005 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (31219) covalent geometry : angle 0.58487 / 0.29 (42232) hydrogen bonds : bond 0.03110 / 2.12 ( 1278) hydrogen bonds : angle 4.25814 / 3.02 ( 3642) Misc. bond : bond 0.00134 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9030 (t) REVERT: B 241 ASP cc_start: 0.8740 (t0) cc_final: 0.8515 (t0) REVERT: B 331 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8767 (tm-30) REVERT: B 441 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8124 (mtm110) REVERT: B 455 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8347 (ttpp) REVERT: B 459 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 603 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7161 (p90) REVERT: B 605 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8516 (p90) REVERT: B 636 MET cc_start: 0.9046 (mmm) cc_final: 0.8771 (mmt) REVERT: C 422 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7695 (mtp85) REVERT: D 631 MET cc_start: 0.8905 (ptt) cc_final: 0.8665 (ptt) REVERT: D 718 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8704 (pt) REVERT: E 603 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7160 (p90) REVERT: E 631 MET cc_start: 0.8224 (ppp) cc_final: 0.7988 (ppp) REVERT: E 636 MET cc_start: 0.8788 (mmp) cc_final: 0.8380 (mmp) REVERT: F 207 GLU cc_start: 0.7869 (mp0) cc_final: 0.7658 (mm-30) REVERT: F 304 LEU cc_start: 0.8635 (tp) cc_final: 0.8303 (pp) REVERT: F 324 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.6965 (tp) REVERT: F 679 ASP cc_start: 0.7457 (t0) cc_final: 0.6850 (t0) outliers start: 63 outliers final: 41 residues processed: 199 average time/residue: 0.1837 time to fit residues: 61.3488 Evaluate side-chains 182 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 342 optimal weight: 0.4980 chunk 226 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 338 optimal weight: 0.9990 chunk 329 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.064485 restraints weight = 101429.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065920 restraints weight = 55466.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.066899 restraints weight = 36968.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067492 restraints weight = 28446.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067800 restraints weight = 24385.307| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31223 Z= 0.149 Angle : 0.616 13.222 42232 Z= 0.300 Chirality : 0.043 0.240 4822 Planarity : 0.004 0.085 5533 Dihedral : 13.350 178.212 4756 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 1.78 % Allowed : 17.34 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3890 helix: 0.78 (0.13), residues: 1931 sheet: -1.90 (0.23), residues: 448 loop : -1.69 (0.17), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 409 TYR 0.011 0.001 TYR D 251 PHE 0.019 0.001 PHE B 605 TRP 0.012 0.001 TRP D 545 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (31219) covalent geometry : angle 0.61636 / 0.30 (42232) hydrogen bonds : bond 0.03336 / 2.28 ( 1278) hydrogen bonds : angle 4.31122 / 3.06 ( 3642) Misc. bond : bond 0.00146 / 0.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9011 (t) REVERT: B 331 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: B 441 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8156 (mtm110) REVERT: B 455 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8337 (ttpp) REVERT: B 459 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8220 (tp) REVERT: B 603 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.7224 (p90) REVERT: B 605 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.8501 (p90) REVERT: B 636 MET cc_start: 0.9084 (mmm) cc_final: 0.8546 (mmt) REVERT: C 422 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7691 (mtp85) REVERT: D 631 MET cc_start: 0.8892 (ptt) cc_final: 0.8677 (ptt) REVERT: D 718 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8808 (pt) REVERT: E 603 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7183 (p90) REVERT: E 636 MET cc_start: 0.8780 (mmp) cc_final: 0.8358 (mmp) REVERT: F 207 GLU cc_start: 0.7884 (mp0) cc_final: 0.7673 (mm-30) REVERT: F 304 LEU cc_start: 0.8700 (tp) cc_final: 0.8354 (pp) REVERT: F 324 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.6961 (tp) outliers start: 57 outliers final: 42 residues processed: 181 average time/residue: 0.1877 time to fit residues: 56.5401 Evaluate side-chains 180 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 349 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 314 optimal weight: 20.0000 chunk 276 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.094889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064425 restraints weight = 100994.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.065792 restraints weight = 54805.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066764 restraints weight = 36738.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067323 restraints weight = 28302.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067703 restraints weight = 24316.873| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31223 Z= 0.149 Angle : 0.617 13.176 42232 Z= 0.300 Chirality : 0.043 0.237 4822 Planarity : 0.004 0.084 5533 Dihedral : 13.367 177.826 4756 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.25 % Favored : 91.67 % Rotamer: Outliers : 1.68 % Allowed : 17.31 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3890 helix: 0.82 (0.13), residues: 1928 sheet: -1.88 (0.23), residues: 449 loop : -1.68 (0.17), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 409 TYR 0.011 0.001 TYR D 251 PHE 0.020 0.001 PHE B 605 TRP 0.013 0.001 TRP D 545 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31219) covalent geometry : angle 0.61708 / 0.30 (42232) hydrogen bonds : bond 0.03349 / 2.29 ( 1278) hydrogen bonds : angle 4.30691 / 3.06 ( 3642) Misc. bond : bond 0.00144 / 0.07 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7780 Ramachandran restraints generated. 3890 Oldfield, 0 Emsley, 3890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9031 (t) REVERT: B 331 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8757 (tm-30) REVERT: B 441 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8192 (mtm110) REVERT: B 455 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8260 (ttpp) REVERT: B 459 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8245 (tp) REVERT: B 603 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 605 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9010 (p90) REVERT: B 636 MET cc_start: 0.9085 (mmm) cc_final: 0.8655 (mmm) REVERT: C 422 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7640 (mtp85) REVERT: D 631 MET cc_start: 0.8901 (ptt) cc_final: 0.8683 (ptt) REVERT: D 636 MET cc_start: 0.8824 (mmm) cc_final: 0.8547 (tpp) REVERT: D 718 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8785 (pt) REVERT: E 603 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7203 (p90) REVERT: E 636 MET cc_start: 0.8793 (mmp) cc_final: 0.8377 (mmp) REVERT: F 304 LEU cc_start: 0.8747 (tp) cc_final: 0.8392 (pp) REVERT: F 324 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7191 (tp) REVERT: F 679 ASP cc_start: 0.8252 (m-30) cc_final: 0.7606 (m-30) REVERT: I 229 MET cc_start: 0.1802 (tpt) cc_final: 0.1580 (tpt) outliers start: 54 outliers final: 40 residues processed: 179 average time/residue: 0.1893 time to fit residues: 56.7256 Evaluate side-chains 175 residues out of total 3208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 555 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 422 ARG Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 605 PHE Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 836 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 603 PHE Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 355 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 828 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 66 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 315 optimal weight: 0.0030 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 359 optimal weight: 9.9990 chunk 387 optimal weight: 6.9990 chunk 222 optimal weight: 0.0670 chunk 232 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 overall best weight: 0.8132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.096342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067538 restraints weight = 101128.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069555 restraints weight = 55926.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069154 restraints weight = 33451.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069596 restraints weight = 29958.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069753 restraints weight = 27075.036| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 31223 Z= 0.103 Angle : 0.587 13.512 42232 Z= 0.284 Chirality : 0.042 0.223 4822 Planarity : 0.004 0.079 5533 Dihedral : 13.270 175.907 4756 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.02 % Favored : 91.90 % Rotamer: Outliers : 1.47 % Allowed : 17.75 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3890 helix: 0.93 (0.13), residues: 1921 sheet: -1.77 (0.23), residues: 449 loop : -1.59 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 332 TYR 0.012 0.001 TYR F 381 PHE 0.017 0.001 PHE D 623 TRP 0.015 0.001 TRP D 545 HIS 0.005 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (31219) covalent geometry : angle 0.58742 / 0.28 (42232) hydrogen bonds : bond 0.02972 / 2.02 ( 1278) hydrogen bonds : angle 4.18104 / 2.96 ( 3642) Misc. bond : bond 0.00125 / 0.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.95 seconds wall clock time: 94 minutes 50.04 seconds (5690.04 seconds total)