Starting phenix.real_space_refine on Thu Mar 5 18:55:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.map" model { file = "/net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wgc_21662/03_2026/6wgc_21662.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 93 5.49 5 S 114 5.16 5 C 15526 2.51 5 N 4101 2.21 5 O 4771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24605 Number of models: 1 Model: "" Number of chains: 15 Chain: "9" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2976 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3386 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 419} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2663 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4505 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 529} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 3425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3425 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 400} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3551 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1315 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "3" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "7" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 831 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "9" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.20 Number of scatterers: 24605 At special positions: 0 Unit cell: (163.75, 127.07, 165.06, 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 114 16.00 P 93 15.00 O 4771 8.00 N 4101 7.00 C 15526 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=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 927.1 milliseconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5444 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 17 sheets defined 56.5% alpha, 6.0% beta 41 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain '9' and resid 59 through 65 removed outlier: 4.011A pdb=" N GLN 9 63 " --> pdb=" O LYS 9 59 " (cutoff:3.500A) Processing helix chain '9' and resid 84 through 92 removed outlier: 3.621A pdb=" N VAL 9 88 " --> pdb=" O GLU 9 84 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN 9 90 " --> pdb=" O GLU 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 113 through 129 removed outlier: 3.623A pdb=" N LEU 9 118 " --> pdb=" O LYS 9 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP 9 119 " --> pdb=" O THR 9 115 " (cutoff:3.500A) Processing helix chain '9' and resid 180 through 185 Processing helix chain '9' and resid 186 through 189 Processing helix chain '9' and resid 194 through 199 removed outlier: 4.385A pdb=" N GLN 9 198 " --> pdb=" O GLY 9 194 " (cutoff:3.500A) Processing helix chain '9' and resid 201 through 207 removed outlier: 3.946A pdb=" N GLN 9 206 " --> pdb=" O MET 9 202 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 9 207 " --> pdb=" O GLN 9 203 " (cutoff:3.500A) Processing helix chain '9' and resid 225 through 230 Processing helix chain '9' and resid 237 through 247 removed outlier: 3.563A pdb=" N LEU 9 247 " --> pdb=" O LEU 9 243 " (cutoff:3.500A) Processing helix chain '9' and resid 296 through 303 Processing helix chain '9' and resid 313 through 323 Processing helix chain '9' and resid 337 through 348 Processing helix chain '9' and resid 388 through 399 removed outlier: 4.065A pdb=" N SER 9 395 " --> pdb=" O ALA 9 391 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS 9 396 " --> pdb=" O LYS 9 392 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE 9 397 " --> pdb=" O VAL 9 393 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN 9 399 " --> pdb=" O SER 9 395 " (cutoff:3.500A) Processing helix chain '9' and resid 404 through 409 Processing helix chain '9' and resid 411 through 425 removed outlier: 3.697A pdb=" N ILE 9 422 " --> pdb=" O LEU 9 418 " (cutoff:3.500A) Processing helix chain '9' and resid 432 through 445 Processing helix chain '9' and resid 454 through 468 removed outlier: 3.512A pdb=" N CYS 9 462 " --> pdb=" O PHE 9 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR 9 463 " --> pdb=" O LEU 9 459 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS 9 468 " --> pdb=" O ILE 9 464 " (cutoff:3.500A) Processing helix chain '9' and resid 495 through 503 removed outlier: 3.943A pdb=" N ASP 9 500 " --> pdb=" O ARG 9 496 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU 9 501 " --> pdb=" O GLU 9 497 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 9 503 " --> pdb=" O TYR 9 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 430 removed outlier: 3.540A pdb=" N LYS A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.817A pdb=" N ALA A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 removed outlier: 4.083A pdb=" N VAL A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.692A pdb=" N THR A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 removed outlier: 3.592A pdb=" N MET A 543 " --> pdb=" O TRP A 539 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 4.095A pdb=" N VAL A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 573 " --> pdb=" O ALA A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 569 through 573' Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.866A pdb=" N ASN A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 583 " --> pdb=" O MET A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 617 removed outlier: 3.839A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.605A pdb=" N ILE A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 638 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.644A pdb=" N LYS A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 726 removed outlier: 3.574A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 785 removed outlier: 4.278A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 835 removed outlier: 3.732A pdb=" N ILE A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.676A pdb=" N ASN A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.566A pdb=" N ALA B 266 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 282 removed outlier: 3.674A pdb=" N VAL B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 removed outlier: 3.502A pdb=" N ILE B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.697A pdb=" N THR B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.635A pdb=" N LYS B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 383 removed outlier: 4.130A pdb=" N VAL B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 4.208A pdb=" N GLU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.951A pdb=" N PHE B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 3.759A pdb=" N MET B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 518 through 532 removed outlier: 3.828A pdb=" N LYS B 522 " --> pdb=" O THR B 518 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 571 through 585 removed outlier: 3.876A pdb=" N MET B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.882A pdb=" N GLU B 610 " --> pdb=" O TYR B 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 92 removed outlier: 4.284A pdb=" N LEU C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 157 removed outlier: 3.818A pdb=" N MET C 142 " --> pdb=" O ASN C 138 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 removed outlier: 3.739A pdb=" N GLU C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.537A pdb=" N ILE C 221 " --> pdb=" O ASP C 217 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 removed outlier: 3.549A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 251 " --> pdb=" O ILE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.567A pdb=" N LEU C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 removed outlier: 3.641A pdb=" N THR C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.706A pdb=" N PHE C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 332 removed outlier: 3.608A pdb=" N PHE C 330 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.847A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 3.721A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.589A pdb=" N LYS C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 385 through 395 removed outlier: 4.357A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 416 removed outlier: 3.913A pdb=" N ARG C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 412 " --> pdb=" O PHE C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.762A pdb=" N ASP C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.641A pdb=" N LEU C 465 " --> pdb=" O PHE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 480 removed outlier: 3.507A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 removed outlier: 3.511A pdb=" N SER C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 3.667A pdb=" N ASP C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 537 through 548 removed outlier: 3.713A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 558 removed outlier: 4.223A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 4.129A pdb=" N LEU C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 588 removed outlier: 3.856A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 592 removed outlier: 4.006A pdb=" N GLU C 592 " --> pdb=" O PHE C 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 589 through 592' Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.583A pdb=" N LYS E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 69 through 87 removed outlier: 3.735A pdb=" N GLN E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 87 " --> pdb=" O TYR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.608A pdb=" N LEU E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL E 109 " --> pdb=" O PRO E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 120 Processing helix chain 'E' and resid 151 through 156 removed outlier: 3.533A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 151 through 156' Processing helix chain 'E' and resid 175 through 183 removed outlier: 4.191A pdb=" N SER E 180 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR E 181 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 210 removed outlier: 3.501A pdb=" N SER E 198 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET E 203 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 210 " --> pdb=" O CYS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 228 through 244 removed outlier: 3.539A pdb=" N VAL E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 Processing helix chain 'E' and resid 255 through 272 removed outlier: 3.591A pdb=" N ASP E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Proline residue: E 267 - end of helix removed outlier: 4.086A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 294 removed outlier: 3.965A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 294 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 384 through 393 removed outlier: 3.903A pdb=" N ALA E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.626A pdb=" N LEU E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER E 425 " --> pdb=" O PHE E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.589A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU E 464 " --> pdb=" O LYS E 460 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.567A pdb=" N GLN D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 91 removed outlier: 4.033A pdb=" N GLN D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.688A pdb=" N ASP D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.214A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN D 152 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.869A pdb=" N SER D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.570A pdb=" N TYR D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.914A pdb=" N TYR D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 280 through 293 removed outlier: 4.119A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.700A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 330 removed outlier: 3.564A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.886A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 removed outlier: 3.589A pdb=" N LEU D 354 " --> pdb=" O ASN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.962A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 Processing helix chain 'D' and resid 384 through 399 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.555A pdb=" N GLU D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 465 removed outlier: 4.036A pdb=" N ASN D 462 " --> pdb=" O ASN D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.712A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.606A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.624A pdb=" N LEU D 513 " --> pdb=" O ILE D 509 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.270A pdb=" N GLN D 528 " --> pdb=" O TYR D 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.583A pdb=" N ILE F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 310 removed outlier: 3.662A pdb=" N LYS F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.830A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS F 321 " --> pdb=" O TRP F 317 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS F 327 " --> pdb=" O LEU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 341 through 354 removed outlier: 3.614A pdb=" N PHE F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 removed outlier: 3.725A pdb=" N ILE F 363 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 387 removed outlier: 3.847A pdb=" N ILE F 384 " --> pdb=" O ARG F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 Processing helix chain 'F' and resid 414 through 430 removed outlier: 3.560A pdb=" N MET F 427 " --> pdb=" O LYS F 423 " (cutoff:3.500A) Processing helix chain '3' and resid 893 through 906 removed outlier: 3.733A pdb=" N ILE 3 900 " --> pdb=" O ILE 3 896 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 3 902 " --> pdb=" O GLY 3 898 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR 3 906 " --> pdb=" O ARG 3 902 " (cutoff:3.500A) Processing helix chain '3' and resid 916 through 921 Processing helix chain '3' and resid 936 through 948 removed outlier: 3.888A pdb=" N LYS 3 943 " --> pdb=" O LEU 3 939 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE 3 944 " --> pdb=" O ALA 3 940 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 3 945 " --> pdb=" O GLY 3 941 " (cutoff:3.500A) Processing helix chain '7' and resid 743 through 755 Processing helix chain '7' and resid 765 through 769 removed outlier: 3.505A pdb=" N THR 7 768 " --> pdb=" O ILE 7 765 " (cutoff:3.500A) Processing helix chain '7' and resid 775 through 786 removed outlier: 4.132A pdb=" N LEU 7 779 " --> pdb=" O THR 7 775 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN 7 784 " --> pdb=" O SER 7 780 " (cutoff:3.500A) Processing helix chain '7' and resid 787 through 790 Processing sheet with id=AA1, first strand: chain '9' and resid 104 through 106 removed outlier: 3.701A pdb=" N TYR 9 105 " --> pdb=" O GLN 9 284 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE 9 286 " --> pdb=" O TYR 9 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '9' and resid 169 through 171 removed outlier: 6.712A pdb=" N ILE 9 170 " --> pdb=" O ASP 9 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '9' and resid 471 through 475 Processing sheet with id=AA4, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA5, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.983A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 598 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 475 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AA7, first strand: chain 'A' and resid 819 through 821 removed outlier: 3.541A pdb=" N GLN A 820 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 476 through 479 removed outlier: 6.454A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 106 removed outlier: 6.566A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.510A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB5, first strand: chain 'D' and resid 127 through 133 Processing sheet with id=AB6, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.432A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB8, first strand: chain '3' and resid 914 through 915 872 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7720 1.36 - 1.50: 7370 1.50 - 1.65: 9954 1.65 - 1.79: 97 1.79 - 1.94: 90 Bond restraints: 25231 Sorted by residual: bond pdb=" C LYS 9 509 " pdb=" N PRO 9 510 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" C LEU C 131 " pdb=" N THR C 132 " ideal model delta sigma weight residual 1.331 1.240 0.091 2.83e-02 1.25e+03 1.04e+01 bond pdb=" C ALA C 372 " pdb=" N PRO C 373 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 5.05e+00 bond pdb=" C MET 9 225 " pdb=" N ASP 9 226 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.35e-02 5.49e+03 4.72e+00 bond pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.39e-02 5.18e+03 4.66e+00 ... (remaining 25226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 33264 2.30 - 4.60: 1021 4.60 - 6.90: 113 6.90 - 9.19: 39 9.19 - 11.49: 5 Bond angle restraints: 34442 Sorted by residual: angle pdb=" C LEU 9 282 " pdb=" N PRO 9 283 " pdb=" CA PRO 9 283 " ideal model delta sigma weight residual 119.84 131.33 -11.49 1.25e+00 6.40e-01 8.45e+01 angle pdb=" N ILE F 411 " pdb=" CA ILE F 411 " pdb=" C ILE F 411 " ideal model delta sigma weight residual 113.16 104.07 9.09 1.49e+00 4.50e-01 3.72e+01 angle pdb=" C ASN 9 232 " pdb=" N THR 9 233 " pdb=" CA THR 9 233 " ideal model delta sigma weight residual 121.31 129.56 -8.25 1.49e+00 4.50e-01 3.07e+01 angle pdb=" C ILE 9 311 " pdb=" N PHE 9 312 " pdb=" CA PHE 9 312 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C ILE D 341 " pdb=" N ILE D 342 " pdb=" CA ILE D 342 " ideal model delta sigma weight residual 120.33 124.63 -4.30 8.00e-01 1.56e+00 2.88e+01 ... (remaining 34437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 13675 25.88 - 51.76: 1286 51.76 - 77.65: 182 77.65 - 103.53: 16 103.53 - 129.41: 2 Dihedral angle restraints: 15161 sinusoidal: 6838 harmonic: 8323 Sorted by residual: dihedral pdb=" CA PHE E 381 " pdb=" C PHE E 381 " pdb=" N ALA E 382 " pdb=" CA ALA E 382 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP 3 955 " pdb=" C ASP 3 955 " pdb=" N ASP 3 956 " pdb=" CA ASP 3 956 " ideal model delta harmonic sigma weight residual -180.00 -151.85 -28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ILE 9 311 " pdb=" C ILE 9 311 " pdb=" N PHE 9 312 " pdb=" CA PHE 9 312 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 15158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3597 0.088 - 0.176: 329 0.176 - 0.264: 27 0.264 - 0.353: 3 0.353 - 0.441: 1 Chirality restraints: 3957 Sorted by residual: chirality pdb=" CB ILE D 508 " pdb=" CA ILE D 508 " pdb=" CG1 ILE D 508 " pdb=" CG2 ILE D 508 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB VAL C 288 " pdb=" CA VAL C 288 " pdb=" CG1 VAL C 288 " pdb=" CG2 VAL C 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB ILE A 578 " pdb=" CA ILE A 578 " pdb=" CG1 ILE A 578 " pdb=" CG2 ILE A 578 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 3954 not shown) Planarity restraints: 4024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 372 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 373 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 373 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 373 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 9 509 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO 9 510 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO 9 510 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 9 510 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 480 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO A 481 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.035 5.00e-02 4.00e+02 ... (remaining 4021 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 3 2.23 - 2.89: 9618 2.89 - 3.56: 36871 3.56 - 4.23: 59429 4.23 - 4.90: 92682 Nonbonded interactions: 198603 Sorted by model distance: nonbonded pdb=" CB THR A 538 " pdb=" OP2 DA G 11 " model vdw 1.558 3.470 nonbonded pdb=" O LEU E 444 " pdb=" CD PRO E 446 " model vdw 1.610 3.440 nonbonded pdb=" CB THR A 538 " pdb=" P DA G 11 " model vdw 2.196 3.830 nonbonded pdb=" O1B AGS A2001 " pdb=" O2A AGS A2001 " model vdw 2.250 3.040 nonbonded pdb=" O1A AGS E2001 " pdb=" O2B AGS E2001 " model vdw 2.280 3.040 ... (remaining 198598 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.530 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25231 Z= 0.293 Angle : 0.990 11.492 34442 Z= 0.573 Chirality : 0.054 0.441 3957 Planarity : 0.006 0.080 4024 Dihedral : 18.907 129.412 9717 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.27 % Favored : 92.62 % Rotamer: Outliers : 0.04 % Allowed : 12.00 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.72 (0.12), residues: 2738 helix: -3.77 (0.08), residues: 1352 sheet: -2.16 (0.31), residues: 237 loop : -2.29 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 332 TYR 0.026 0.002 TYR 3 938 PHE 0.029 0.002 PHE 9 256 TRP 0.022 0.002 TRP C 58 HIS 0.011 0.002 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00605 (25231) covalent geometry : angle 0.98999 (34442) hydrogen bonds : bond 0.30110 ( 955) hydrogen bonds : angle 9.30857 ( 2696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 1.138 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: 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: 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: 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: symmetry clash REVERT: 9 180 SER cc_start: 0.8700 (m) cc_final: 0.8468 (p) REVERT: 9 204 HIS cc_start: 0.8398 (m170) cc_final: 0.7900 (m170) REVERT: 9 222 LEU cc_start: 0.9678 (tp) cc_final: 0.9441 (tp) REVERT: 9 244 GLU cc_start: 0.8011 (pt0) cc_final: 0.7056 (pt0) REVERT: 9 322 LYS cc_start: 0.8663 (mttp) cc_final: 0.8415 (mttp) REVERT: 9 423 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8328 (tp-100) REVERT: 9 435 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8389 (pt0) REVERT: 9 440 TYR cc_start: 0.9443 (t80) cc_final: 0.9111 (t80) REVERT: 9 498 PHE cc_start: 0.9163 (m-80) cc_final: 0.8888 (m-10) REVERT: A 491 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 564 LEU cc_start: 0.8959 (mp) cc_final: 0.8182 (pp) REVERT: A 571 MET cc_start: 0.8780 (mtm) cc_final: 0.7933 (mtt) REVERT: A 582 PHE cc_start: 0.8857 (m-80) cc_final: 0.8397 (m-80) REVERT: A 585 TRP cc_start: 0.9063 (m-10) cc_final: 0.8532 (m-90) REVERT: A 602 MET cc_start: 0.8086 (tpp) cc_final: 0.7630 (tpp) REVERT: A 623 MET cc_start: 0.8658 (tpt) cc_final: 0.8400 (tpt) REVERT: A 866 TRP cc_start: 0.8445 (t60) cc_final: 0.8034 (t60) REVERT: A 879 LEU cc_start: 0.9464 (mm) cc_final: 0.8995 (mm) REVERT: A 881 LYS cc_start: 0.9513 (tmmt) cc_final: 0.9311 (tmtt) REVERT: A 900 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8049 (mm-30) REVERT: A 902 LYS cc_start: 0.9273 (mtpt) cc_final: 0.8670 (mttt) REVERT: B 315 LEU cc_start: 0.9686 (tp) cc_final: 0.9455 (tt) REVERT: B 377 LYS cc_start: 0.9341 (mtmt) cc_final: 0.8785 (mmtm) REVERT: B 411 TYR cc_start: 0.8411 (m-10) cc_final: 0.7452 (m-10) REVERT: B 440 MET cc_start: 0.8761 (tmm) cc_final: 0.8433 (tmm) REVERT: B 441 LEU cc_start: 0.9425 (mm) cc_final: 0.8565 (mt) REVERT: B 460 TYR cc_start: 0.9269 (m-10) cc_final: 0.9031 (m-10) REVERT: B 466 ASP cc_start: 0.8674 (p0) cc_final: 0.8209 (p0) REVERT: B 496 MET cc_start: 0.7428 (ppp) cc_final: 0.6824 (tmm) REVERT: B 524 MET cc_start: 0.8345 (ptm) cc_final: 0.7488 (ptt) REVERT: B 547 ARG cc_start: 0.3938 (tmt-80) cc_final: 0.3298 (ptm160) REVERT: B 561 HIS cc_start: 0.9177 (m170) cc_final: 0.8628 (t-90) REVERT: B 578 MET cc_start: 0.8307 (ptp) cc_final: 0.7501 (ptm) REVERT: B 581 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 604 TYR cc_start: 0.8294 (m-10) cc_final: 0.7944 (m-10) REVERT: C 111 ASP cc_start: 0.8445 (p0) cc_final: 0.8061 (p0) REVERT: C 201 MET cc_start: 0.8828 (ptt) cc_final: 0.8525 (ptt) REVERT: C 206 LYS cc_start: 0.9005 (mmmm) cc_final: 0.8138 (mtmm) REVERT: C 207 ASP cc_start: 0.8013 (t0) cc_final: 0.7589 (t0) REVERT: C 214 ASN cc_start: 0.8734 (p0) cc_final: 0.8148 (t0) REVERT: C 292 LEU cc_start: 0.9172 (tp) cc_final: 0.8909 (tp) REVERT: C 296 ASP cc_start: 0.9362 (p0) cc_final: 0.8767 (p0) REVERT: C 297 ARG cc_start: 0.8896 (mtp180) cc_final: 0.8503 (mtm-85) REVERT: C 321 LEU cc_start: 0.9364 (mm) cc_final: 0.9143 (mm) REVERT: C 371 HIS cc_start: 0.8675 (m-70) cc_final: 0.8408 (m90) REVERT: C 540 PHE cc_start: 0.8753 (t80) cc_final: 0.8365 (t80) REVERT: E 110 LYS cc_start: 0.9302 (tmtt) cc_final: 0.8736 (tppt) REVERT: E 170 MET cc_start: 0.8747 (ptp) cc_final: 0.8531 (ptp) REVERT: E 195 ASP cc_start: 0.9184 (p0) cc_final: 0.8821 (p0) REVERT: E 323 ASP cc_start: 0.7414 (t0) cc_final: 0.7153 (t0) REVERT: E 336 TYR cc_start: 0.8904 (t80) cc_final: 0.8269 (t80) REVERT: E 422 GLN cc_start: 0.9141 (tp40) cc_final: 0.8243 (tp-100) REVERT: D 105 GLN cc_start: 0.9344 (mm110) cc_final: 0.9086 (mm-40) REVERT: D 123 TYR cc_start: 0.9180 (m-80) cc_final: 0.8569 (m-80) REVERT: D 218 GLU cc_start: 0.8866 (mp0) cc_final: 0.8242 (mp0) REVERT: D 233 ASN cc_start: 0.8598 (m110) cc_final: 0.8397 (t0) REVERT: D 253 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8000 (mtmt) REVERT: D 259 TYR cc_start: 0.9144 (m-10) cc_final: 0.8702 (m-10) REVERT: D 262 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8087 (tptp) REVERT: D 268 PHE cc_start: 0.8951 (t80) cc_final: 0.8684 (t80) REVERT: D 270 GLN cc_start: 0.9020 (mm110) cc_final: 0.8698 (tm-30) REVERT: D 313 LEU cc_start: 0.9260 (tp) cc_final: 0.9011 (tp) REVERT: D 365 ASP cc_start: 0.8301 (m-30) cc_final: 0.8053 (m-30) REVERT: D 390 ILE cc_start: 0.9423 (mt) cc_final: 0.9172 (tp) REVERT: D 425 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8170 (tpm170) REVERT: D 467 ASP cc_start: 0.8574 (m-30) cc_final: 0.8358 (m-30) REVERT: D 469 PHE cc_start: 0.8513 (m-80) cc_final: 0.8253 (m-80) REVERT: D 475 VAL cc_start: 0.8708 (t) cc_final: 0.7681 (m) REVERT: D 496 MET cc_start: 0.7828 (mmt) cc_final: 0.7498 (mmm) REVERT: D 506 MET cc_start: 0.7749 (tpp) cc_final: 0.7310 (tpp) REVERT: D 512 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7579 (mm-30) REVERT: F 337 ARG cc_start: 0.6212 (mmt90) cc_final: 0.5373 (ttp-170) REVERT: F 364 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8427 (mp0) REVERT: F 398 ILE cc_start: 0.9442 (pt) cc_final: 0.9232 (pt) REVERT: 3 909 PHE cc_start: 0.7542 (m-80) cc_final: 0.7074 (m-80) REVERT: 3 921 GLU cc_start: 0.9059 (pt0) cc_final: 0.8188 (pt0) REVERT: 3 922 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8265 (mmt90) REVERT: 3 952 MET cc_start: 0.8081 (mmt) cc_final: 0.7745 (mtp) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.1852 time to fit residues: 163.9987 Evaluate side-chains 406 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 232 ASN 9 295 GLN 9 388 ASN 9 401 ASN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 ASN A 581 ASN A 725 HIS B 279 ASN B 297 GLN B 310 GLN B 426 ASN B 493 GLN C 63 GLN C 69 HIS C 78 ASN C 253 GLN C 282 GLN C 423 ASN E 52 ASN E 114 ASN E 223 GLN D 58 GLN D 80 GLN D 105 GLN D 158 HIS ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 ASN 3 924 ASN 3 950 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.104169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080580 restraints weight = 101649.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082162 restraints weight = 58714.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083370 restraints weight = 40385.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083505 restraints weight = 34750.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083699 restraints weight = 31337.229| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.150 Angle : 0.681 7.829 34442 Z= 0.365 Chirality : 0.043 0.213 3957 Planarity : 0.005 0.089 4024 Dihedral : 17.715 131.688 4026 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.12 % Allowed : 6.51 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -3.40 (0.14), residues: 2738 helix: -2.31 (0.11), residues: 1465 sheet: -1.82 (0.31), residues: 226 loop : -1.99 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 218 TYR 0.024 0.002 TYR B 411 PHE 0.020 0.001 PHE D 135 TRP 0.018 0.002 TRP A 529 HIS 0.009 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00313 (25231) covalent geometry : angle 0.68083 (34442) hydrogen bonds : bond 0.06047 ( 955) hydrogen bonds : angle 5.50666 ( 2696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 560 time to evaluate : 0.946 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 104 LEU cc_start: 0.7433 (mt) cc_final: 0.7086 (mt) REVERT: 9 201 ASN cc_start: 0.8806 (t0) cc_final: 0.8488 (t0) REVERT: 9 204 HIS cc_start: 0.8319 (m170) cc_final: 0.7545 (m170) REVERT: 9 244 GLU cc_start: 0.8258 (pt0) cc_final: 0.7429 (pt0) REVERT: 9 261 MET cc_start: 0.7673 (mpp) cc_final: 0.6835 (mpp) REVERT: 9 324 CYS cc_start: 0.8163 (p) cc_final: 0.7935 (p) REVERT: 9 346 GLU cc_start: 0.6494 (tp30) cc_final: 0.6066 (tm-30) REVERT: 9 423 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8261 (tp-100) REVERT: 9 435 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8334 (pt0) REVERT: 9 440 TYR cc_start: 0.9410 (t80) cc_final: 0.8520 (t80) REVERT: 9 485 PHE cc_start: 0.5803 (m-80) cc_final: 0.5542 (m-10) REVERT: 9 498 PHE cc_start: 0.8991 (m-80) cc_final: 0.8716 (m-10) REVERT: 9 499 TYR cc_start: 0.9099 (m-10) cc_final: 0.8553 (m-80) REVERT: 9 502 MET cc_start: 0.9055 (ppp) cc_final: 0.8790 (mmt) REVERT: A 526 GLU cc_start: 0.8989 (pt0) cc_final: 0.8224 (mp0) REVERT: A 564 LEU cc_start: 0.8986 (mp) cc_final: 0.8199 (pp) REVERT: A 571 MET cc_start: 0.8711 (mtm) cc_final: 0.7243 (mtt) REVERT: A 578 ILE cc_start: 0.8900 (tt) cc_final: 0.8163 (tt) REVERT: A 579 MET cc_start: 0.8695 (mmp) cc_final: 0.8161 (mmp) REVERT: A 602 MET cc_start: 0.8151 (tpp) cc_final: 0.7537 (tpp) REVERT: A 623 MET cc_start: 0.8560 (tpt) cc_final: 0.8347 (tpt) REVERT: A 696 VAL cc_start: 0.9608 (t) cc_final: 0.9351 (p) REVERT: A 879 LEU cc_start: 0.9229 (mm) cc_final: 0.8787 (mm) REVERT: A 884 MET cc_start: 0.8677 (mmm) cc_final: 0.8467 (mmm) REVERT: A 902 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8524 (mtmt) REVERT: B 269 VAL cc_start: 0.8270 (t) cc_final: 0.7252 (t) REVERT: B 273 GLU cc_start: 0.9265 (tt0) cc_final: 0.8953 (tt0) REVERT: B 360 CYS cc_start: 0.7927 (m) cc_final: 0.7685 (m) REVERT: B 377 LYS cc_start: 0.9450 (mtmt) cc_final: 0.8796 (mptt) REVERT: B 417 ASP cc_start: 0.7594 (t0) cc_final: 0.5610 (p0) REVERT: B 440 MET cc_start: 0.8788 (tmm) cc_final: 0.8375 (tmm) REVERT: B 458 HIS cc_start: 0.8180 (t-90) cc_final: 0.7688 (t70) REVERT: B 496 MET cc_start: 0.7340 (ppp) cc_final: 0.6117 (tmm) REVERT: B 547 ARG cc_start: 0.3746 (tmt-80) cc_final: 0.3338 (ptm160) REVERT: B 561 HIS cc_start: 0.9204 (m170) cc_final: 0.8553 (t-170) REVERT: B 563 CYS cc_start: 0.9275 (m) cc_final: 0.9030 (m) REVERT: B 578 MET cc_start: 0.8148 (ptp) cc_final: 0.7660 (ptm) REVERT: C 83 LEU cc_start: 0.8831 (pp) cc_final: 0.8547 (pp) REVERT: C 106 PHE cc_start: 0.8543 (m-80) cc_final: 0.8333 (m-80) REVERT: C 113 THR cc_start: 0.7609 (p) cc_final: 0.7328 (p) REVERT: C 206 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8396 (mttp) REVERT: C 213 PHE cc_start: 0.8974 (m-80) cc_final: 0.8425 (m-10) REVERT: C 214 ASN cc_start: 0.8676 (p0) cc_final: 0.8400 (t0) REVERT: C 297 ARG cc_start: 0.8989 (mtp180) cc_final: 0.8769 (mtm-85) REVERT: C 321 LEU cc_start: 0.9645 (mm) cc_final: 0.9415 (mm) REVERT: C 361 MET cc_start: 0.8879 (ptp) cc_final: 0.8408 (ptp) REVERT: C 371 HIS cc_start: 0.8603 (m-70) cc_final: 0.8400 (m90) REVERT: C 523 GLN cc_start: 0.8212 (pt0) cc_final: 0.7617 (pt0) REVERT: C 540 PHE cc_start: 0.8793 (t80) cc_final: 0.8389 (t80) REVERT: E 110 LYS cc_start: 0.9372 (tmtt) cc_final: 0.8815 (tppt) REVERT: E 139 GLN cc_start: 0.8671 (pm20) cc_final: 0.8391 (pm20) REVERT: E 169 THR cc_start: 0.9698 (m) cc_final: 0.9334 (p) REVERT: E 170 MET cc_start: 0.8629 (ptp) cc_final: 0.8347 (ptp) REVERT: E 195 ASP cc_start: 0.8911 (p0) cc_final: 0.8698 (p0) REVERT: E 260 ASP cc_start: 0.8276 (p0) cc_final: 0.7404 (t0) REVERT: E 336 TYR cc_start: 0.8835 (t80) cc_final: 0.8444 (t80) REVERT: E 376 LEU cc_start: 0.9181 (mp) cc_final: 0.8979 (mt) REVERT: E 422 GLN cc_start: 0.9148 (tp40) cc_final: 0.8421 (tp40) REVERT: E 473 TYR cc_start: 0.8612 (m-80) cc_final: 0.8164 (m-80) REVERT: D 105 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8815 (mm-40) REVERT: D 123 TYR cc_start: 0.9041 (m-80) cc_final: 0.8370 (m-80) REVERT: D 229 THR cc_start: 0.9128 (p) cc_final: 0.8837 (p) REVERT: D 248 PHE cc_start: 0.9185 (m-80) cc_final: 0.8530 (m-80) REVERT: D 259 TYR cc_start: 0.9148 (m-10) cc_final: 0.8625 (m-10) REVERT: D 268 PHE cc_start: 0.8829 (t80) cc_final: 0.8217 (t80) REVERT: D 313 LEU cc_start: 0.9209 (tp) cc_final: 0.8926 (tp) REVERT: D 326 MET cc_start: 0.8852 (mtp) cc_final: 0.8521 (mtp) REVERT: D 365 ASP cc_start: 0.8301 (m-30) cc_final: 0.8045 (m-30) REVERT: D 372 LEU cc_start: 0.9298 (tp) cc_final: 0.9060 (tt) REVERT: D 390 ILE cc_start: 0.9463 (mt) cc_final: 0.9186 (tp) REVERT: D 455 ASP cc_start: 0.8486 (p0) cc_final: 0.8280 (p0) REVERT: D 461 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8466 (tt0) REVERT: D 462 ASN cc_start: 0.9533 (m-40) cc_final: 0.9298 (m-40) REVERT: D 467 ASP cc_start: 0.8603 (m-30) cc_final: 0.8098 (m-30) REVERT: D 496 MET cc_start: 0.7850 (mmp) cc_final: 0.7578 (mmp) REVERT: D 506 MET cc_start: 0.7630 (tpp) cc_final: 0.7207 (tpp) REVERT: D 512 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8029 (mm-30) REVERT: F 304 ASP cc_start: 0.9297 (t0) cc_final: 0.9086 (m-30) REVERT: F 331 VAL cc_start: 0.9470 (p) cc_final: 0.9223 (p) REVERT: F 332 PHE cc_start: 0.9250 (m-10) cc_final: 0.8876 (m-80) REVERT: F 335 ARG cc_start: 0.9101 (mtt-85) cc_final: 0.8554 (mmm160) REVERT: F 336 ARG cc_start: 0.9033 (mtp-110) cc_final: 0.8361 (ttm110) REVERT: F 337 ARG cc_start: 0.6443 (mmt90) cc_final: 0.5523 (ttp-170) REVERT: F 350 MET cc_start: 0.9406 (tmm) cc_final: 0.9110 (tmm) REVERT: F 354 MET cc_start: 0.8246 (mmp) cc_final: 0.7858 (mmp) REVERT: F 364 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8673 (mp0) REVERT: F 410 ASN cc_start: 0.8576 (m-40) cc_final: 0.8315 (t0) outliers start: 3 outliers final: 0 residues processed: 562 average time/residue: 0.1655 time to fit residues: 145.0118 Evaluate side-chains 414 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 203 GLN ** 9 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN 9 401 ASN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 852 GLN B 449 GLN C 63 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 440 ASN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 ASN ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 949 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.103421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080131 restraints weight = 102087.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081623 restraints weight = 59872.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082669 restraints weight = 41541.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082852 restraints weight = 36102.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082979 restraints weight = 32708.055| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25231 Z= 0.155 Angle : 0.644 10.277 34442 Z= 0.345 Chirality : 0.043 0.165 3957 Planarity : 0.004 0.067 4024 Dihedral : 17.534 134.813 4026 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: -2.62 (0.15), residues: 2738 helix: -1.55 (0.12), residues: 1485 sheet: -1.66 (0.32), residues: 226 loop : -1.79 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 227 TYR 0.019 0.002 TYR 9 291 PHE 0.034 0.001 PHE F 389 TRP 0.013 0.001 TRP C 494 HIS 0.005 0.001 HIS 9 230 Details of bonding type rmsd covalent geometry : bond 0.00335 (25231) covalent geometry : angle 0.64418 (34442) hydrogen bonds : bond 0.05136 ( 955) hydrogen bonds : angle 5.08872 ( 2696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 515 time to evaluate : 1.001 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 180 SER cc_start: 0.9439 (p) cc_final: 0.8794 (p) REVERT: 9 184 LYS cc_start: 0.9390 (mmtm) cc_final: 0.9064 (mmtt) REVERT: 9 201 ASN cc_start: 0.8774 (t0) cc_final: 0.8272 (t0) REVERT: 9 204 HIS cc_start: 0.8267 (m170) cc_final: 0.7508 (m170) REVERT: 9 222 LEU cc_start: 0.9613 (tp) cc_final: 0.9405 (tp) REVERT: 9 259 ILE cc_start: 0.9016 (mp) cc_final: 0.8727 (mp) REVERT: 9 261 MET cc_start: 0.7505 (mpp) cc_final: 0.6819 (mpp) REVERT: 9 322 LYS cc_start: 0.8669 (mttp) cc_final: 0.8347 (mttp) REVERT: 9 346 GLU cc_start: 0.6672 (tp30) cc_final: 0.6462 (tm-30) REVERT: 9 419 CYS cc_start: 0.9516 (t) cc_final: 0.8728 (t) REVERT: 9 423 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8338 (tp-100) REVERT: 9 435 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8342 (pt0) REVERT: 9 499 TYR cc_start: 0.9135 (m-10) cc_final: 0.8425 (m-80) REVERT: 9 502 MET cc_start: 0.9070 (ppp) cc_final: 0.8788 (mmt) REVERT: 9 511 PHE cc_start: 0.7626 (t80) cc_final: 0.7390 (t80) REVERT: A 526 GLU cc_start: 0.8895 (pt0) cc_final: 0.8048 (tp30) REVERT: A 543 MET cc_start: 0.9430 (ptm) cc_final: 0.9109 (ptm) REVERT: A 564 LEU cc_start: 0.9119 (mp) cc_final: 0.8443 (pp) REVERT: A 567 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8414 (mm-30) REVERT: A 571 MET cc_start: 0.8686 (mtm) cc_final: 0.8020 (mtp) REVERT: A 578 ILE cc_start: 0.9089 (tt) cc_final: 0.8818 (tt) REVERT: A 623 MET cc_start: 0.8546 (tpt) cc_final: 0.8240 (tpp) REVERT: A 682 LEU cc_start: 0.8754 (tp) cc_final: 0.8503 (tt) REVERT: A 879 LEU cc_start: 0.9212 (mm) cc_final: 0.8831 (mm) REVERT: A 881 LYS cc_start: 0.9530 (tmmt) cc_final: 0.9104 (tmtt) REVERT: A 902 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8575 (mtmt) REVERT: B 273 GLU cc_start: 0.8967 (tt0) cc_final: 0.8708 (tt0) REVERT: B 360 CYS cc_start: 0.7869 (m) cc_final: 0.7639 (m) REVERT: B 377 LYS cc_start: 0.9454 (mtmt) cc_final: 0.9235 (mtmt) REVERT: B 417 ASP cc_start: 0.7586 (t0) cc_final: 0.5528 (p0) REVERT: B 440 MET cc_start: 0.8770 (tmm) cc_final: 0.8377 (tmm) REVERT: B 496 MET cc_start: 0.7092 (ppp) cc_final: 0.5877 (tmm) REVERT: B 559 PHE cc_start: 0.9084 (t80) cc_final: 0.8858 (t80) REVERT: B 561 HIS cc_start: 0.9194 (m170) cc_final: 0.8336 (t-170) REVERT: B 563 CYS cc_start: 0.9058 (m) cc_final: 0.8594 (m) REVERT: B 604 TYR cc_start: 0.8201 (m-10) cc_final: 0.7802 (m-10) REVERT: C 202 VAL cc_start: 0.8935 (p) cc_final: 0.8598 (p) REVERT: C 206 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8497 (mttp) REVERT: C 213 PHE cc_start: 0.9087 (m-80) cc_final: 0.8663 (m-10) REVERT: C 214 ASN cc_start: 0.8713 (p0) cc_final: 0.8369 (t0) REVERT: C 321 LEU cc_start: 0.9529 (mm) cc_final: 0.9313 (mm) REVERT: C 361 MET cc_start: 0.8955 (ptp) cc_final: 0.8555 (ptp) REVERT: C 523 GLN cc_start: 0.8221 (pt0) cc_final: 0.7649 (pt0) REVERT: C 540 PHE cc_start: 0.8835 (t80) cc_final: 0.8437 (t80) REVERT: E 169 THR cc_start: 0.9695 (m) cc_final: 0.9327 (p) REVERT: E 170 MET cc_start: 0.8650 (ptp) cc_final: 0.8386 (ptp) REVERT: E 195 ASP cc_start: 0.8983 (p0) cc_final: 0.8735 (p0) REVERT: E 210 MET cc_start: 0.9382 (mtm) cc_final: 0.9026 (mmp) REVERT: E 422 GLN cc_start: 0.9386 (mm110) cc_final: 0.8972 (mm-40) REVERT: E 473 TYR cc_start: 0.8587 (m-80) cc_final: 0.8166 (m-80) REVERT: D 123 TYR cc_start: 0.9059 (m-80) cc_final: 0.8550 (m-80) REVERT: D 237 MET cc_start: 0.8563 (tpp) cc_final: 0.8330 (tpp) REVERT: D 246 CYS cc_start: 0.7675 (p) cc_final: 0.7436 (p) REVERT: D 248 PHE cc_start: 0.9166 (m-80) cc_final: 0.8407 (m-80) REVERT: D 253 LYS cc_start: 0.8923 (mmtt) cc_final: 0.7891 (mtmt) REVERT: D 259 TYR cc_start: 0.9189 (m-10) cc_final: 0.8706 (m-10) REVERT: D 262 LYS cc_start: 0.8448 (tmtt) cc_final: 0.8180 (tmtt) REVERT: D 268 PHE cc_start: 0.8707 (t80) cc_final: 0.8232 (t80) REVERT: D 326 MET cc_start: 0.8768 (mtp) cc_final: 0.8326 (ttt) REVERT: D 338 LYS cc_start: 0.9303 (ttpt) cc_final: 0.8748 (ptpt) REVERT: D 365 ASP cc_start: 0.8310 (m-30) cc_final: 0.8045 (m-30) REVERT: D 467 ASP cc_start: 0.8318 (m-30) cc_final: 0.7871 (m-30) REVERT: D 512 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7987 (mm-30) REVERT: F 304 ASP cc_start: 0.9312 (t0) cc_final: 0.9110 (m-30) REVERT: F 335 ARG cc_start: 0.9076 (mtt-85) cc_final: 0.8561 (mmm160) REVERT: F 337 ARG cc_start: 0.5887 (mmt90) cc_final: 0.5298 (ttm170) REVERT: F 350 MET cc_start: 0.9456 (tmm) cc_final: 0.9164 (tmm) REVERT: F 354 MET cc_start: 0.8177 (mmp) cc_final: 0.7920 (mmp) REVERT: F 356 THR cc_start: 0.6263 (p) cc_final: 0.6031 (p) REVERT: F 410 ASN cc_start: 0.8531 (m-40) cc_final: 0.8166 (t0) REVERT: F 419 ASN cc_start: 0.9383 (m-40) cc_final: 0.9135 (m110) REVERT: 3 909 PHE cc_start: 0.7693 (m-80) cc_final: 0.7027 (m-80) outliers start: 1 outliers final: 0 residues processed: 516 average time/residue: 0.1665 time to fit residues: 133.8774 Evaluate side-chains 391 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 252 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 273 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 230 HIS ** 9 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN 9 413 GLN B 398 ASN C 63 GLN C 312 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 233 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079872 restraints weight = 98141.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081874 restraints weight = 61119.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083268 restraints weight = 43133.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.084150 restraints weight = 33331.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.084872 restraints weight = 27810.676| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.128 Angle : 0.614 9.708 34442 Z= 0.325 Chirality : 0.042 0.188 3957 Planarity : 0.004 0.069 4024 Dihedral : 17.391 134.654 4026 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.19 (0.15), residues: 2738 helix: -1.14 (0.13), residues: 1489 sheet: -1.58 (0.32), residues: 228 loop : -1.66 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 227 TYR 0.024 0.001 TYR 9 291 PHE 0.021 0.001 PHE F 389 TRP 0.029 0.001 TRP A 529 HIS 0.005 0.001 HIS A 777 Details of bonding type rmsd covalent geometry : bond 0.00278 (25231) covalent geometry : angle 0.61367 (34442) hydrogen bonds : bond 0.04483 ( 955) hydrogen bonds : angle 4.82557 ( 2696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 506 time to evaluate : 1.298 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 184 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9073 (mmtt) REVERT: 9 201 ASN cc_start: 0.8763 (t0) cc_final: 0.8119 (t0) REVERT: 9 204 HIS cc_start: 0.7839 (m170) cc_final: 0.6948 (m170) REVERT: 9 222 LEU cc_start: 0.9606 (tp) cc_final: 0.9399 (tp) REVERT: 9 224 GLU cc_start: 0.7609 (tp30) cc_final: 0.7322 (tp30) REVERT: 9 244 GLU cc_start: 0.8245 (pt0) cc_final: 0.7635 (pt0) REVERT: 9 258 LEU cc_start: 0.9199 (mt) cc_final: 0.8973 (mp) REVERT: 9 261 MET cc_start: 0.7714 (mpp) cc_final: 0.7130 (mpp) REVERT: 9 322 LYS cc_start: 0.8612 (mttp) cc_final: 0.8130 (mttp) REVERT: 9 346 GLU cc_start: 0.6646 (tp30) cc_final: 0.6422 (tm-30) REVERT: 9 423 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8373 (tp-100) REVERT: 9 435 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8318 (pt0) REVERT: 9 495 MET cc_start: 0.6891 (pmm) cc_final: 0.6470 (pmm) REVERT: 9 498 PHE cc_start: 0.8925 (m-10) cc_final: 0.8542 (m-10) REVERT: 9 499 TYR cc_start: 0.9069 (m-10) cc_final: 0.8293 (m-80) REVERT: A 526 GLU cc_start: 0.8851 (pt0) cc_final: 0.8186 (mp0) REVERT: A 543 MET cc_start: 0.9502 (ptm) cc_final: 0.9200 (ptm) REVERT: A 546 LEU cc_start: 0.9447 (mt) cc_final: 0.9176 (mp) REVERT: A 567 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8501 (mm-30) REVERT: A 571 MET cc_start: 0.8334 (mtm) cc_final: 0.7984 (mtp) REVERT: A 623 MET cc_start: 0.8402 (tpt) cc_final: 0.8157 (tpp) REVERT: A 682 LEU cc_start: 0.8699 (tp) cc_final: 0.8438 (tt) REVERT: A 696 VAL cc_start: 0.9532 (t) cc_final: 0.9318 (p) REVERT: A 843 MET cc_start: 0.8957 (mpp) cc_final: 0.8577 (mpp) REVERT: A 879 LEU cc_start: 0.9264 (mm) cc_final: 0.8913 (mm) REVERT: A 881 LYS cc_start: 0.9547 (tmmt) cc_final: 0.9136 (tmtt) REVERT: A 902 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8548 (mttt) REVERT: B 269 VAL cc_start: 0.8185 (t) cc_final: 0.7471 (t) REVERT: B 440 MET cc_start: 0.8712 (tmm) cc_final: 0.8293 (tmm) REVERT: B 458 HIS cc_start: 0.8274 (t-90) cc_final: 0.7641 (t70) REVERT: B 460 TYR cc_start: 0.9070 (m-10) cc_final: 0.8831 (m-10) REVERT: B 496 MET cc_start: 0.6950 (ppp) cc_final: 0.5550 (tmm) REVERT: B 561 HIS cc_start: 0.9192 (m170) cc_final: 0.8378 (t-170) REVERT: B 578 MET cc_start: 0.7774 (ttt) cc_final: 0.7087 (ttt) REVERT: C 206 LYS cc_start: 0.9125 (mmtp) cc_final: 0.8753 (mttp) REVERT: C 213 PHE cc_start: 0.9038 (m-80) cc_final: 0.8648 (m-10) REVERT: C 214 ASN cc_start: 0.8665 (p0) cc_final: 0.8369 (t0) REVERT: C 296 ASP cc_start: 0.9293 (p0) cc_final: 0.9034 (p0) REVERT: C 320 MET cc_start: 0.8613 (ttt) cc_final: 0.8412 (tpp) REVERT: C 361 MET cc_start: 0.8907 (ptp) cc_final: 0.8511 (ptp) REVERT: C 523 GLN cc_start: 0.8088 (pt0) cc_final: 0.7614 (pt0) REVERT: C 540 PHE cc_start: 0.8702 (t80) cc_final: 0.8329 (t80) REVERT: E 170 MET cc_start: 0.8622 (ptp) cc_final: 0.8400 (ptp) REVERT: E 195 ASP cc_start: 0.8949 (p0) cc_final: 0.8690 (p0) REVERT: E 210 MET cc_start: 0.9188 (mtm) cc_final: 0.8586 (mmp) REVERT: E 473 TYR cc_start: 0.8506 (m-80) cc_final: 0.8165 (m-80) REVERT: D 81 GLU cc_start: 0.8423 (tp30) cc_final: 0.8197 (tp30) REVERT: D 123 TYR cc_start: 0.8945 (m-80) cc_final: 0.8537 (m-80) REVERT: D 246 CYS cc_start: 0.7447 (p) cc_final: 0.7097 (p) REVERT: D 248 PHE cc_start: 0.9095 (m-80) cc_final: 0.8286 (m-80) REVERT: D 253 LYS cc_start: 0.8855 (mmtt) cc_final: 0.7882 (mtmt) REVERT: D 259 TYR cc_start: 0.9197 (m-10) cc_final: 0.8607 (m-10) REVERT: D 268 PHE cc_start: 0.8682 (t80) cc_final: 0.8225 (t80) REVERT: D 326 MET cc_start: 0.8981 (mtp) cc_final: 0.8738 (ttt) REVERT: D 334 LEU cc_start: 0.9333 (tp) cc_final: 0.8594 (tp) REVERT: D 338 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8736 (ptpt) REVERT: D 365 ASP cc_start: 0.8048 (m-30) cc_final: 0.7820 (m-30) REVERT: D 390 ILE cc_start: 0.9415 (mt) cc_final: 0.9164 (tp) REVERT: D 467 ASP cc_start: 0.8207 (m-30) cc_final: 0.7812 (m-30) REVERT: D 506 MET cc_start: 0.7558 (tpp) cc_final: 0.7319 (tpp) REVERT: D 512 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8107 (mm-30) REVERT: F 335 ARG cc_start: 0.9043 (mtt-85) cc_final: 0.8571 (mmm160) REVERT: F 336 ARG cc_start: 0.9084 (mtp-110) cc_final: 0.8821 (mtp-110) REVERT: F 337 ARG cc_start: 0.5777 (mmt90) cc_final: 0.5451 (ptm160) REVERT: F 350 MET cc_start: 0.9466 (tmm) cc_final: 0.9205 (tmm) REVERT: F 354 MET cc_start: 0.7985 (mmp) cc_final: 0.7749 (mmp) REVERT: F 364 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8597 (mp0) REVERT: F 410 ASN cc_start: 0.8440 (m-40) cc_final: 0.8195 (t0) REVERT: F 419 ASN cc_start: 0.9402 (m-40) cc_final: 0.9132 (m110) REVERT: 3 909 PHE cc_start: 0.7701 (m-80) cc_final: 0.7097 (m-80) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.1609 time to fit residues: 127.9825 Evaluate side-chains 388 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 110 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 253 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 0.0170 chunk 213 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 chunk 197 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 426 ASN B 471 GLN C 22 HIS C 63 GLN C 312 HIS C 371 HIS E 58 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN E 238 ASN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080940 restraints weight = 99898.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082971 restraints weight = 61426.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084359 restraints weight = 43268.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085353 restraints weight = 33575.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.085922 restraints weight = 27974.755| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.119 Angle : 0.608 8.669 34442 Z= 0.318 Chirality : 0.042 0.229 3957 Planarity : 0.004 0.062 4024 Dihedral : 17.209 133.126 4026 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.90 (0.15), residues: 2738 helix: -0.92 (0.13), residues: 1474 sheet: -1.30 (0.32), residues: 235 loop : -1.54 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 448 TYR 0.020 0.001 TYR 9 291 PHE 0.023 0.001 PHE D 72 TRP 0.019 0.001 TRP B 305 HIS 0.005 0.001 HIS A 777 Details of bonding type rmsd covalent geometry : bond 0.00254 (25231) covalent geometry : angle 0.60770 (34442) hydrogen bonds : bond 0.04186 ( 955) hydrogen bonds : angle 4.61851 ( 2696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 521 time to evaluate : 0.948 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8586 (mmp) cc_final: 0.8277 (mmm) REVERT: 9 120 MET cc_start: 0.8726 (tmm) cc_final: 0.8245 (tmm) REVERT: 9 183 GLN cc_start: 0.9384 (mm110) cc_final: 0.9179 (mm110) REVERT: 9 184 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9091 (mmtt) REVERT: 9 201 ASN cc_start: 0.8776 (t0) cc_final: 0.8143 (t0) REVERT: 9 204 HIS cc_start: 0.7789 (m170) cc_final: 0.6983 (m170) REVERT: 9 224 GLU cc_start: 0.7747 (tp30) cc_final: 0.7413 (tp30) REVERT: 9 244 GLU cc_start: 0.8208 (pt0) cc_final: 0.7789 (pt0) REVERT: 9 261 MET cc_start: 0.7651 (mpp) cc_final: 0.7186 (mpp) REVERT: 9 296 MET cc_start: 0.5731 (mtt) cc_final: 0.5334 (mmt) REVERT: 9 322 LYS cc_start: 0.8641 (mttp) cc_final: 0.8001 (pttt) REVERT: 9 323 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8236 (mmmt) REVERT: 9 419 CYS cc_start: 0.9467 (t) cc_final: 0.8678 (t) REVERT: 9 423 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8399 (tp-100) REVERT: 9 435 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8251 (pt0) REVERT: 9 440 TYR cc_start: 0.9155 (t80) cc_final: 0.8595 (t80) REVERT: 9 498 PHE cc_start: 0.8644 (m-10) cc_final: 0.8427 (m-10) REVERT: 9 499 TYR cc_start: 0.8826 (m-10) cc_final: 0.8160 (m-80) REVERT: A 526 GLU cc_start: 0.8855 (pt0) cc_final: 0.8403 (pm20) REVERT: A 564 LEU cc_start: 0.9151 (mp) cc_final: 0.8556 (pp) REVERT: A 623 MET cc_start: 0.8240 (tpt) cc_final: 0.7991 (tmm) REVERT: A 682 LEU cc_start: 0.8667 (tp) cc_final: 0.8386 (tt) REVERT: A 696 VAL cc_start: 0.9508 (t) cc_final: 0.9292 (p) REVERT: A 722 MET cc_start: 0.7457 (tpt) cc_final: 0.6483 (tpt) REVERT: A 843 MET cc_start: 0.8708 (mpp) cc_final: 0.8302 (mpp) REVERT: A 879 LEU cc_start: 0.9239 (mm) cc_final: 0.8888 (mm) REVERT: A 881 LYS cc_start: 0.9502 (tmmt) cc_final: 0.9137 (tmtt) REVERT: A 902 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8731 (ttpp) REVERT: B 269 VAL cc_start: 0.8613 (t) cc_final: 0.7754 (t) REVERT: B 300 MET cc_start: 0.8844 (ptm) cc_final: 0.8600 (ptp) REVERT: B 377 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8700 (mmtm) REVERT: B 417 ASP cc_start: 0.7692 (t70) cc_final: 0.5907 (p0) REVERT: B 440 MET cc_start: 0.8622 (tmm) cc_final: 0.8247 (tmm) REVERT: B 458 HIS cc_start: 0.8124 (t-90) cc_final: 0.7610 (t70) REVERT: B 460 TYR cc_start: 0.9092 (m-10) cc_final: 0.8827 (m-10) REVERT: B 496 MET cc_start: 0.6657 (ppp) cc_final: 0.5285 (tmm) REVERT: B 561 HIS cc_start: 0.9118 (m170) cc_final: 0.8349 (t-170) REVERT: C 106 PHE cc_start: 0.8529 (m-80) cc_final: 0.8190 (m-80) REVERT: C 111 ASP cc_start: 0.8667 (m-30) cc_final: 0.8399 (m-30) REVERT: C 206 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8897 (mttp) REVERT: C 213 PHE cc_start: 0.9065 (m-80) cc_final: 0.8823 (m-80) REVERT: C 215 THR cc_start: 0.8800 (m) cc_final: 0.8425 (m) REVERT: C 296 ASP cc_start: 0.9291 (p0) cc_final: 0.9029 (p0) REVERT: C 361 MET cc_start: 0.8890 (ptp) cc_final: 0.8495 (ptp) REVERT: C 498 LEU cc_start: 0.9090 (mm) cc_final: 0.8517 (mm) REVERT: C 523 GLN cc_start: 0.7984 (pt0) cc_final: 0.7590 (pt0) REVERT: C 540 PHE cc_start: 0.8716 (t80) cc_final: 0.8332 (t80) REVERT: C 585 MET cc_start: 0.6835 (ttt) cc_final: 0.5731 (tmm) REVERT: E 170 MET cc_start: 0.8542 (ptp) cc_final: 0.8340 (ptp) REVERT: E 183 CYS cc_start: 0.8959 (m) cc_final: 0.8566 (t) REVERT: E 195 ASP cc_start: 0.8934 (p0) cc_final: 0.8661 (p0) REVERT: E 210 MET cc_start: 0.9158 (mtm) cc_final: 0.8452 (mmp) REVERT: E 473 TYR cc_start: 0.8451 (m-80) cc_final: 0.8055 (m-80) REVERT: D 123 TYR cc_start: 0.8911 (m-80) cc_final: 0.8639 (m-80) REVERT: D 253 LYS cc_start: 0.8781 (mmtt) cc_final: 0.7849 (mtmt) REVERT: D 259 TYR cc_start: 0.9165 (m-10) cc_final: 0.8470 (m-10) REVERT: D 268 PHE cc_start: 0.8689 (t80) cc_final: 0.8206 (t80) REVERT: D 365 ASP cc_start: 0.8064 (m-30) cc_final: 0.7818 (m-30) REVERT: D 390 ILE cc_start: 0.9386 (mt) cc_final: 0.9169 (tp) REVERT: D 461 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8618 (tt0) REVERT: D 467 ASP cc_start: 0.8118 (m-30) cc_final: 0.7620 (m-30) REVERT: D 506 MET cc_start: 0.7597 (tpp) cc_final: 0.7273 (tpp) REVERT: D 508 ILE cc_start: 0.9713 (tt) cc_final: 0.9251 (tt) REVERT: D 512 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8059 (mm-30) REVERT: F 332 PHE cc_start: 0.9172 (m-80) cc_final: 0.8955 (m-80) REVERT: F 335 ARG cc_start: 0.9033 (mtt-85) cc_final: 0.8417 (mmm160) REVERT: F 336 ARG cc_start: 0.9045 (mtp-110) cc_final: 0.8825 (mtp-110) REVERT: F 337 ARG cc_start: 0.5992 (mmt90) cc_final: 0.5653 (ptm160) REVERT: F 354 MET cc_start: 0.8009 (mmp) cc_final: 0.7784 (mmp) REVERT: F 364 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8592 (mp0) REVERT: F 398 ILE cc_start: 0.9462 (pt) cc_final: 0.9237 (pt) REVERT: F 410 ASN cc_start: 0.8132 (m-40) cc_final: 0.7834 (t0) REVERT: F 419 ASN cc_start: 0.9407 (m-40) cc_final: 0.9109 (m110) REVERT: 3 909 PHE cc_start: 0.7540 (m-80) cc_final: 0.7055 (m-80) outliers start: 1 outliers final: 0 residues processed: 522 average time/residue: 0.1628 time to fit residues: 133.3461 Evaluate side-chains 397 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 3 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 278 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN B 426 ASN B 472 ASN C 63 GLN C 312 HIS C 383 ASN E 32 ASN E 58 HIS ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN D 137 HIS ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.102487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079419 restraints weight = 103335.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080858 restraints weight = 60106.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081633 restraints weight = 43037.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082081 restraints weight = 37408.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.082247 restraints weight = 32915.449| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25231 Z= 0.186 Angle : 0.639 11.585 34442 Z= 0.340 Chirality : 0.043 0.175 3957 Planarity : 0.004 0.064 4024 Dihedral : 17.210 132.827 4026 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.63 (0.16), residues: 2738 helix: -0.71 (0.13), residues: 1478 sheet: -1.28 (0.32), residues: 236 loop : -1.38 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 317 TYR 0.017 0.002 TYR D 61 PHE 0.031 0.002 PHE B 475 TRP 0.023 0.002 TRP A 529 HIS 0.010 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00401 (25231) covalent geometry : angle 0.63929 (34442) hydrogen bonds : bond 0.04352 ( 955) hydrogen bonds : angle 4.73261 ( 2696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 484 time to evaluate : 0.926 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 184 LYS cc_start: 0.9379 (mmtm) cc_final: 0.9156 (mmtt) REVERT: 9 201 ASN cc_start: 0.8685 (t0) cc_final: 0.8161 (t0) REVERT: 9 204 HIS cc_start: 0.8005 (m170) cc_final: 0.7250 (m170) REVERT: 9 222 LEU cc_start: 0.9599 (tp) cc_final: 0.9345 (tp) REVERT: 9 224 GLU cc_start: 0.7780 (tp30) cc_final: 0.7387 (tp30) REVERT: 9 244 GLU cc_start: 0.8269 (pt0) cc_final: 0.7638 (pt0) REVERT: 9 259 ILE cc_start: 0.9064 (mp) cc_final: 0.8815 (mp) REVERT: 9 261 MET cc_start: 0.7988 (mpp) cc_final: 0.7281 (mpp) REVERT: 9 296 MET cc_start: 0.6107 (mtt) cc_final: 0.5658 (mmt) REVERT: 9 322 LYS cc_start: 0.8710 (mttp) cc_final: 0.8082 (tttt) REVERT: 9 324 CYS cc_start: 0.8230 (p) cc_final: 0.8026 (p) REVERT: 9 435 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8201 (pt0) REVERT: 9 499 TYR cc_start: 0.8927 (m-10) cc_final: 0.8282 (m-80) REVERT: A 524 CYS cc_start: 0.9315 (m) cc_final: 0.9095 (m) REVERT: A 526 GLU cc_start: 0.8774 (pt0) cc_final: 0.8356 (pm20) REVERT: A 564 LEU cc_start: 0.9249 (mp) cc_final: 0.8541 (pp) REVERT: A 578 ILE cc_start: 0.9277 (tt) cc_final: 0.8978 (tt) REVERT: A 600 ASN cc_start: 0.8346 (t0) cc_final: 0.8140 (p0) REVERT: A 606 GLU cc_start: 0.9144 (mp0) cc_final: 0.8926 (mp0) REVERT: A 623 MET cc_start: 0.8218 (tpt) cc_final: 0.7927 (tmm) REVERT: A 696 VAL cc_start: 0.9599 (t) cc_final: 0.9397 (p) REVERT: A 808 LEU cc_start: 0.9390 (pp) cc_final: 0.9190 (tp) REVERT: A 879 LEU cc_start: 0.9305 (mm) cc_final: 0.8973 (mm) REVERT: A 893 LYS cc_start: 0.9328 (tttt) cc_final: 0.9088 (ttmm) REVERT: A 902 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8767 (ttpp) REVERT: B 377 LYS cc_start: 0.9283 (mtmt) cc_final: 0.8710 (mmtm) REVERT: B 460 TYR cc_start: 0.9055 (m-10) cc_final: 0.8791 (m-10) REVERT: B 496 MET cc_start: 0.6803 (ppp) cc_final: 0.5708 (tmm) REVERT: B 561 HIS cc_start: 0.9115 (m170) cc_final: 0.8333 (t-170) REVERT: B 563 CYS cc_start: 0.8828 (t) cc_final: 0.8505 (p) REVERT: C 206 LYS cc_start: 0.9179 (mmtp) cc_final: 0.8839 (mttp) REVERT: C 361 MET cc_start: 0.8926 (ptp) cc_final: 0.8588 (ptp) REVERT: C 523 GLN cc_start: 0.8061 (pt0) cc_final: 0.7602 (pt0) REVERT: C 540 PHE cc_start: 0.8690 (t80) cc_final: 0.8309 (t80) REVERT: E 183 CYS cc_start: 0.8837 (m) cc_final: 0.8517 (t) REVERT: E 195 ASP cc_start: 0.8920 (p0) cc_final: 0.8613 (p0) REVERT: E 210 MET cc_start: 0.9072 (mtm) cc_final: 0.8311 (mmp) REVERT: E 473 TYR cc_start: 0.8543 (m-80) cc_final: 0.8121 (m-80) REVERT: D 123 TYR cc_start: 0.8977 (m-80) cc_final: 0.8631 (m-80) REVERT: D 246 CYS cc_start: 0.7516 (p) cc_final: 0.7115 (p) REVERT: D 248 PHE cc_start: 0.9011 (m-80) cc_final: 0.8283 (m-80) REVERT: D 253 LYS cc_start: 0.8789 (mmtt) cc_final: 0.7907 (mtmt) REVERT: D 259 TYR cc_start: 0.9120 (m-10) cc_final: 0.8546 (m-10) REVERT: D 262 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7916 (pttm) REVERT: D 268 PHE cc_start: 0.8783 (t80) cc_final: 0.8258 (t80) REVERT: D 365 ASP cc_start: 0.8016 (m-30) cc_final: 0.7783 (m-30) REVERT: D 390 ILE cc_start: 0.9418 (mt) cc_final: 0.9165 (tp) REVERT: D 467 ASP cc_start: 0.8143 (m-30) cc_final: 0.7709 (m-30) REVERT: D 506 MET cc_start: 0.7404 (tpp) cc_final: 0.7168 (tpp) REVERT: D 512 GLU cc_start: 0.8524 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 332 PHE cc_start: 0.9183 (m-80) cc_final: 0.8759 (m-80) REVERT: F 335 ARG cc_start: 0.9054 (mtt-85) cc_final: 0.8561 (mmm160) REVERT: F 336 ARG cc_start: 0.9032 (mtp-110) cc_final: 0.8817 (mtp-110) REVERT: F 337 ARG cc_start: 0.5785 (mmt90) cc_final: 0.5458 (ptm160) REVERT: F 350 MET cc_start: 0.9390 (tmm) cc_final: 0.9145 (tmm) REVERT: F 354 MET cc_start: 0.8106 (mmp) cc_final: 0.7830 (mmp) REVERT: F 364 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8609 (mp0) REVERT: F 398 ILE cc_start: 0.9499 (pt) cc_final: 0.9259 (pt) REVERT: F 419 ASN cc_start: 0.9404 (m-40) cc_final: 0.9085 (m110) REVERT: 3 909 PHE cc_start: 0.7663 (m-80) cc_final: 0.7185 (m-80) outliers start: 1 outliers final: 0 residues processed: 485 average time/residue: 0.1662 time to fit residues: 126.6540 Evaluate side-chains 385 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 201 optimal weight: 2.9990 chunk 182 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 278 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 413 GLN ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN C 63 GLN C 383 ASN E 58 HIS E 82 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 GLN ** D 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.102729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079527 restraints weight = 102658.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.081203 restraints weight = 60169.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082210 restraints weight = 41299.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.082450 restraints weight = 35676.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.082572 restraints weight = 31793.352| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25231 Z= 0.149 Angle : 0.629 10.890 34442 Z= 0.329 Chirality : 0.043 0.221 3957 Planarity : 0.004 0.064 4024 Dihedral : 17.159 132.622 4026 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.49 (0.16), residues: 2738 helix: -0.60 (0.13), residues: 1469 sheet: -1.23 (0.34), residues: 226 loop : -1.31 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 287 TYR 0.016 0.001 TYR 9 291 PHE 0.032 0.001 PHE B 475 TRP 0.016 0.001 TRP F 378 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00328 (25231) covalent geometry : angle 0.62891 (34442) hydrogen bonds : bond 0.04194 ( 955) hydrogen bonds : angle 4.64161 ( 2696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 0.849 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8572 (mmp) cc_final: 0.8237 (mmm) REVERT: 9 184 LYS cc_start: 0.9324 (mmtm) cc_final: 0.9056 (mmtt) REVERT: 9 201 ASN cc_start: 0.8769 (t0) cc_final: 0.8219 (t0) REVERT: 9 204 HIS cc_start: 0.7895 (m170) cc_final: 0.7083 (m170) REVERT: 9 222 LEU cc_start: 0.9598 (tp) cc_final: 0.9329 (tp) REVERT: 9 224 GLU cc_start: 0.7922 (tp30) cc_final: 0.7685 (tp30) REVERT: 9 225 MET cc_start: 0.8591 (ttp) cc_final: 0.8366 (ttp) REVERT: 9 244 GLU cc_start: 0.8110 (pt0) cc_final: 0.7824 (pt0) REVERT: 9 259 ILE cc_start: 0.8972 (mp) cc_final: 0.8699 (mp) REVERT: 9 261 MET cc_start: 0.8012 (mpp) cc_final: 0.7379 (mpp) REVERT: 9 296 MET cc_start: 0.5941 (mtt) cc_final: 0.5373 (mmt) REVERT: 9 322 LYS cc_start: 0.8702 (mttp) cc_final: 0.7962 (tttt) REVERT: 9 324 CYS cc_start: 0.8129 (p) cc_final: 0.7906 (p) REVERT: 9 499 TYR cc_start: 0.8970 (m-10) cc_final: 0.8288 (m-80) REVERT: A 526 GLU cc_start: 0.8694 (pt0) cc_final: 0.8313 (pm20) REVERT: A 564 LEU cc_start: 0.9121 (mp) cc_final: 0.8553 (pp) REVERT: A 578 ILE cc_start: 0.9318 (tt) cc_final: 0.9029 (tt) REVERT: A 623 MET cc_start: 0.8220 (tpt) cc_final: 0.7887 (tmm) REVERT: A 696 VAL cc_start: 0.9574 (t) cc_final: 0.9357 (p) REVERT: A 843 MET cc_start: 0.8939 (mpp) cc_final: 0.8510 (mpp) REVERT: A 879 LEU cc_start: 0.9299 (mm) cc_final: 0.8907 (mm) REVERT: A 893 LYS cc_start: 0.9317 (tttt) cc_final: 0.9062 (ttmm) REVERT: A 902 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8790 (ttpp) REVERT: B 300 MET cc_start: 0.8563 (ptp) cc_final: 0.7938 (ptp) REVERT: B 377 LYS cc_start: 0.9285 (mtmt) cc_final: 0.8695 (mmtm) REVERT: B 417 ASP cc_start: 0.7647 (t70) cc_final: 0.5643 (p0) REVERT: B 440 MET cc_start: 0.8624 (tmm) cc_final: 0.8381 (tmm) REVERT: B 458 HIS cc_start: 0.8321 (t-90) cc_final: 0.7884 (t70) REVERT: B 460 TYR cc_start: 0.9094 (m-10) cc_final: 0.8887 (m-10) REVERT: B 466 ASP cc_start: 0.8828 (p0) cc_final: 0.8500 (p0) REVERT: B 496 MET cc_start: 0.6551 (ppp) cc_final: 0.5767 (tmm) REVERT: B 561 HIS cc_start: 0.9113 (m170) cc_final: 0.8379 (t-170) REVERT: B 563 CYS cc_start: 0.8807 (t) cc_final: 0.8531 (p) REVERT: B 611 LYS cc_start: 0.9447 (mmpt) cc_final: 0.9225 (mmmt) REVERT: C 106 PHE cc_start: 0.8586 (m-80) cc_final: 0.8373 (m-80) REVERT: C 204 ASN cc_start: 0.8830 (t0) cc_final: 0.8626 (t0) REVERT: C 206 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8852 (mttp) REVERT: C 361 MET cc_start: 0.8922 (ptp) cc_final: 0.8575 (ptp) REVERT: C 498 LEU cc_start: 0.9345 (mm) cc_final: 0.8827 (mm) REVERT: C 523 GLN cc_start: 0.8014 (pt0) cc_final: 0.7604 (pt0) REVERT: C 540 PHE cc_start: 0.8692 (t80) cc_final: 0.8292 (t80) REVERT: C 585 MET cc_start: 0.7136 (ttt) cc_final: 0.6081 (tmm) REVERT: E 183 CYS cc_start: 0.8824 (m) cc_final: 0.8546 (t) REVERT: E 195 ASP cc_start: 0.8864 (p0) cc_final: 0.8529 (p0) REVERT: E 210 MET cc_start: 0.8849 (mtm) cc_final: 0.8196 (mmp) REVERT: E 454 VAL cc_start: 0.8941 (t) cc_final: 0.8730 (p) REVERT: E 473 TYR cc_start: 0.8512 (m-80) cc_final: 0.8080 (m-80) REVERT: D 86 ILE cc_start: 0.9711 (tp) cc_final: 0.9304 (tp) REVERT: D 123 TYR cc_start: 0.8927 (m-80) cc_final: 0.8599 (m-80) REVERT: D 240 HIS cc_start: 0.8626 (m-70) cc_final: 0.8280 (t-170) REVERT: D 246 CYS cc_start: 0.7568 (p) cc_final: 0.7018 (p) REVERT: D 248 PHE cc_start: 0.8942 (m-80) cc_final: 0.8256 (m-80) REVERT: D 253 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8028 (mtmt) REVERT: D 259 TYR cc_start: 0.9107 (m-10) cc_final: 0.8719 (m-10) REVERT: D 268 PHE cc_start: 0.8816 (t80) cc_final: 0.8319 (t80) REVERT: D 338 LYS cc_start: 0.9454 (ptpt) cc_final: 0.9056 (pttm) REVERT: D 365 ASP cc_start: 0.8032 (m-30) cc_final: 0.7757 (m-30) REVERT: D 390 ILE cc_start: 0.9435 (mt) cc_final: 0.9216 (tp) REVERT: D 467 ASP cc_start: 0.8124 (m-30) cc_final: 0.7608 (m-30) REVERT: D 506 MET cc_start: 0.7565 (tpp) cc_final: 0.7323 (tpp) REVERT: D 512 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 332 PHE cc_start: 0.9239 (m-80) cc_final: 0.8818 (m-80) REVERT: F 335 ARG cc_start: 0.9076 (mtt-85) cc_final: 0.8535 (mmm160) REVERT: F 336 ARG cc_start: 0.9035 (mtp-110) cc_final: 0.8835 (mtp85) REVERT: F 337 ARG cc_start: 0.5743 (mmt90) cc_final: 0.5251 (ttm170) REVERT: F 350 MET cc_start: 0.9340 (tmm) cc_final: 0.9065 (tmm) REVERT: F 354 MET cc_start: 0.8124 (mmp) cc_final: 0.7881 (mmp) REVERT: F 360 ASP cc_start: 0.9072 (p0) cc_final: 0.8636 (p0) REVERT: F 361 ASP cc_start: 0.8506 (p0) cc_final: 0.8111 (p0) REVERT: F 364 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8609 (mp0) REVERT: F 367 LYS cc_start: 0.6814 (mmtt) cc_final: 0.6565 (mmtt) REVERT: F 395 ASP cc_start: 0.8679 (m-30) cc_final: 0.8288 (m-30) REVERT: F 398 ILE cc_start: 0.9482 (pt) cc_final: 0.9277 (pt) REVERT: F 400 ARG cc_start: 0.9459 (ptp-110) cc_final: 0.8867 (mtp85) REVERT: F 410 ASN cc_start: 0.8625 (t0) cc_final: 0.8411 (t0) REVERT: F 419 ASN cc_start: 0.9410 (m-40) cc_final: 0.9061 (m110) REVERT: 3 909 PHE cc_start: 0.7666 (m-80) cc_final: 0.7283 (m-80) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.1694 time to fit residues: 130.5030 Evaluate side-chains 386 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 158 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 383 ASN E 58 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN D 381 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080364 restraints weight = 102593.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.081898 restraints weight = 59330.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083217 restraints weight = 41038.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083324 restraints weight = 34950.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.083395 restraints weight = 31107.317| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25231 Z= 0.134 Angle : 0.621 10.192 34442 Z= 0.324 Chirality : 0.043 0.204 3957 Planarity : 0.004 0.062 4024 Dihedral : 17.089 132.117 4026 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.16), residues: 2738 helix: -0.54 (0.13), residues: 1487 sheet: -1.15 (0.34), residues: 226 loop : -1.31 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 471 TYR 0.022 0.001 TYR B 411 PHE 0.028 0.001 PHE B 475 TRP 0.023 0.002 TRP D 460 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00297 (25231) covalent geometry : angle 0.62113 (34442) hydrogen bonds : bond 0.04088 ( 955) hydrogen bonds : angle 4.57684 ( 2696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.818 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9 89 MET cc_start: 0.8499 (mmp) cc_final: 0.8240 (mmm) REVERT: 9 201 ASN cc_start: 0.8671 (t0) cc_final: 0.8065 (t0) REVERT: 9 204 HIS cc_start: 0.7967 (m170) cc_final: 0.7077 (m170) REVERT: 9 222 LEU cc_start: 0.9583 (tp) cc_final: 0.9297 (tp) REVERT: 9 224 GLU cc_start: 0.8010 (tp30) cc_final: 0.7725 (tp30) REVERT: 9 244 GLU cc_start: 0.8139 (pt0) cc_final: 0.7469 (pt0) REVERT: 9 259 ILE cc_start: 0.8969 (mp) cc_final: 0.8707 (mp) REVERT: 9 261 MET cc_start: 0.7998 (mpp) cc_final: 0.7401 (mpp) REVERT: 9 296 MET cc_start: 0.5923 (mtt) cc_final: 0.5390 (mmt) REVERT: 9 322 LYS cc_start: 0.8676 (mttp) cc_final: 0.8012 (pttp) REVERT: 9 323 LYS cc_start: 0.8461 (mmpt) cc_final: 0.7974 (mmmt) REVERT: 9 499 TYR cc_start: 0.8975 (m-10) cc_final: 0.8312 (m-80) REVERT: A 578 ILE cc_start: 0.9310 (tt) cc_final: 0.8874 (tt) REVERT: A 579 MET cc_start: 0.9016 (mmp) cc_final: 0.8742 (mmm) REVERT: A 608 GLN cc_start: 0.9028 (mp10) cc_final: 0.8515 (mp10) REVERT: A 623 MET cc_start: 0.8233 (tpt) cc_final: 0.7866 (tmm) REVERT: A 696 VAL cc_start: 0.9572 (t) cc_final: 0.9357 (p) REVERT: A 843 MET cc_start: 0.8805 (mpp) cc_final: 0.8262 (mpp) REVERT: A 879 LEU cc_start: 0.9322 (mm) cc_final: 0.8974 (mm) REVERT: A 893 LYS cc_start: 0.9313 (tttt) cc_final: 0.9077 (ttmm) REVERT: A 902 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8799 (ttpp) REVERT: B 300 MET cc_start: 0.8576 (ptp) cc_final: 0.7891 (ptp) REVERT: B 377 LYS cc_start: 0.9281 (mtmt) cc_final: 0.8688 (mmtm) REVERT: B 458 HIS cc_start: 0.8299 (t-90) cc_final: 0.7830 (t70) REVERT: B 466 ASP cc_start: 0.8856 (p0) cc_final: 0.8590 (p0) REVERT: B 496 MET cc_start: 0.6538 (ppp) cc_final: 0.5695 (tmm) REVERT: B 561 HIS cc_start: 0.9108 (m170) cc_final: 0.8401 (t-170) REVERT: B 563 CYS cc_start: 0.8787 (t) cc_final: 0.8568 (p) REVERT: B 611 LYS cc_start: 0.9452 (mmpt) cc_final: 0.9220 (mmmt) REVERT: C 106 PHE cc_start: 0.8600 (m-80) cc_final: 0.8368 (m-80) REVERT: C 204 ASN cc_start: 0.8831 (t0) cc_final: 0.8622 (t0) REVERT: C 206 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8880 (mttp) REVERT: C 296 ASP cc_start: 0.9212 (p0) cc_final: 0.8882 (p0) REVERT: C 361 MET cc_start: 0.8886 (ptp) cc_final: 0.8556 (ptp) REVERT: C 423 ASN cc_start: 0.9534 (t0) cc_final: 0.9332 (t0) REVERT: C 488 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 498 LEU cc_start: 0.9300 (mm) cc_final: 0.8699 (mm) REVERT: C 523 GLN cc_start: 0.7995 (pt0) cc_final: 0.7587 (pt0) REVERT: C 540 PHE cc_start: 0.8714 (t80) cc_final: 0.8298 (t80) REVERT: C 585 MET cc_start: 0.7109 (ttt) cc_final: 0.5808 (tmm) REVERT: E 79 ARG cc_start: 0.8784 (ptp90) cc_final: 0.8367 (ptp-170) REVERT: E 183 CYS cc_start: 0.8756 (m) cc_final: 0.8500 (t) REVERT: E 195 ASP cc_start: 0.8865 (p0) cc_final: 0.8519 (p0) REVERT: E 210 MET cc_start: 0.8835 (mtm) cc_final: 0.8174 (mmp) REVERT: E 473 TYR cc_start: 0.8510 (m-80) cc_final: 0.8071 (m-80) REVERT: D 86 ILE cc_start: 0.9471 (tp) cc_final: 0.9197 (tp) REVERT: D 90 ILE cc_start: 0.9000 (tt) cc_final: 0.8652 (pt) REVERT: D 123 TYR cc_start: 0.8942 (m-80) cc_final: 0.8617 (m-80) REVERT: D 240 HIS cc_start: 0.8508 (m-70) cc_final: 0.8219 (t-170) REVERT: D 248 PHE cc_start: 0.8917 (m-80) cc_final: 0.8300 (m-80) REVERT: D 253 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8023 (mtmt) REVERT: D 259 TYR cc_start: 0.9077 (m-10) cc_final: 0.8702 (m-10) REVERT: D 268 PHE cc_start: 0.8804 (t80) cc_final: 0.8306 (t80) REVERT: D 338 LYS cc_start: 0.9398 (ptpt) cc_final: 0.8928 (pttm) REVERT: D 365 ASP cc_start: 0.7981 (m-30) cc_final: 0.7689 (m-30) REVERT: D 467 ASP cc_start: 0.8206 (m-30) cc_final: 0.7682 (m-30) REVERT: D 496 MET cc_start: 0.8154 (mmp) cc_final: 0.7899 (mmp) REVERT: D 512 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7895 (mm-30) REVERT: F 332 PHE cc_start: 0.9229 (m-80) cc_final: 0.8799 (m-80) REVERT: F 335 ARG cc_start: 0.9068 (mtt-85) cc_final: 0.8532 (mmm160) REVERT: F 336 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8628 (mtp85) REVERT: F 337 ARG cc_start: 0.5698 (mmt90) cc_final: 0.5405 (ptm160) REVERT: F 350 MET cc_start: 0.9357 (tmm) cc_final: 0.9069 (tmm) REVERT: F 354 MET cc_start: 0.8143 (mmp) cc_final: 0.7893 (mmp) REVERT: F 364 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8597 (mp0) REVERT: F 367 LYS cc_start: 0.6868 (mmtt) cc_final: 0.6588 (mmtt) REVERT: F 400 ARG cc_start: 0.9447 (ptp-110) cc_final: 0.8821 (mtp85) REVERT: F 419 ASN cc_start: 0.9382 (m-40) cc_final: 0.9075 (m110) REVERT: 3 909 PHE cc_start: 0.7768 (m-80) cc_final: 0.7375 (m-80) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.1671 time to fit residues: 126.3774 Evaluate side-chains 389 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 191 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 261 optimal weight: 0.0970 chunk 139 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 203 GLN 9 295 GLN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN C 63 GLN C 383 ASN E 58 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.100579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078650 restraints weight = 101899.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.079819 restraints weight = 59291.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080879 restraints weight = 43083.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081237 restraints weight = 35469.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081486 restraints weight = 31578.964| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25231 Z= 0.212 Angle : 0.687 12.654 34442 Z= 0.361 Chirality : 0.044 0.271 3957 Planarity : 0.004 0.063 4024 Dihedral : 17.163 130.848 4026 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.50 (0.16), residues: 2738 helix: -0.55 (0.13), residues: 1482 sheet: -1.27 (0.34), residues: 226 loop : -1.39 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 317 TYR 0.024 0.002 TYR B 411 PHE 0.032 0.002 PHE B 475 TRP 0.022 0.002 TRP D 460 HIS 0.008 0.002 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00462 (25231) covalent geometry : angle 0.68689 (34442) hydrogen bonds : bond 0.04445 ( 955) hydrogen bonds : angle 4.78107 ( 2696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.949 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: 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: 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: symmetry clash REVERT: 9 89 MET cc_start: 0.8480 (mmp) cc_final: 0.8262 (mmm) REVERT: 9 120 MET cc_start: 0.8569 (tmm) cc_final: 0.8126 (tmm) REVERT: 9 201 ASN cc_start: 0.8650 (t0) cc_final: 0.7939 (t0) REVERT: 9 204 HIS cc_start: 0.8076 (m170) cc_final: 0.7215 (m170) REVERT: 9 222 LEU cc_start: 0.9628 (tp) cc_final: 0.9207 (tp) REVERT: 9 224 GLU cc_start: 0.8309 (tp30) cc_final: 0.7900 (tp30) REVERT: 9 229 LEU cc_start: 0.5957 (mt) cc_final: 0.5681 (mt) REVERT: 9 244 GLU cc_start: 0.8041 (pt0) cc_final: 0.7550 (pt0) REVERT: 9 261 MET cc_start: 0.8240 (mpp) cc_final: 0.7234 (mpp) REVERT: 9 474 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8517 (mmtt) REVERT: 9 499 TYR cc_start: 0.9098 (m-10) cc_final: 0.8534 (m-80) REVERT: A 526 GLU cc_start: 0.8706 (pt0) cc_final: 0.8181 (tp30) REVERT: A 600 ASN cc_start: 0.8512 (p0) cc_final: 0.8054 (p0) REVERT: A 608 GLN cc_start: 0.8979 (mp10) cc_final: 0.8545 (mp10) REVERT: A 623 MET cc_start: 0.8250 (tpt) cc_final: 0.7892 (tmm) REVERT: A 843 MET cc_start: 0.8852 (mpp) cc_final: 0.8395 (mpp) REVERT: A 879 LEU cc_start: 0.9338 (mm) cc_final: 0.8906 (mm) REVERT: A 893 LYS cc_start: 0.9349 (tttt) cc_final: 0.9060 (ttmm) REVERT: A 902 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8838 (ttpp) REVERT: B 300 MET cc_start: 0.8863 (ptp) cc_final: 0.8518 (ptp) REVERT: B 377 LYS cc_start: 0.9265 (mtmt) cc_final: 0.8756 (tptt) REVERT: B 381 ASP cc_start: 0.8974 (p0) cc_final: 0.8644 (p0) REVERT: B 440 MET cc_start: 0.8636 (tmm) cc_final: 0.8218 (tmm) REVERT: B 466 ASP cc_start: 0.8852 (p0) cc_final: 0.8581 (p0) REVERT: B 496 MET cc_start: 0.6743 (ppp) cc_final: 0.5850 (tmm) REVERT: B 561 HIS cc_start: 0.9114 (m170) cc_final: 0.8364 (t-170) REVERT: B 563 CYS cc_start: 0.8873 (t) cc_final: 0.8553 (p) REVERT: B 611 LYS cc_start: 0.9470 (mmpt) cc_final: 0.9223 (mmmt) REVERT: C 106 PHE cc_start: 0.8688 (m-80) cc_final: 0.8483 (m-80) REVERT: C 204 ASN cc_start: 0.8849 (t0) cc_final: 0.8637 (t0) REVERT: C 206 LYS cc_start: 0.9190 (mmtp) cc_final: 0.8860 (mttp) REVERT: C 207 ASP cc_start: 0.8326 (t0) cc_final: 0.8125 (t0) REVERT: C 296 ASP cc_start: 0.9222 (p0) cc_final: 0.8876 (p0) REVERT: C 361 MET cc_start: 0.8915 (ptp) cc_final: 0.8596 (ptp) REVERT: C 523 GLN cc_start: 0.8105 (pt0) cc_final: 0.7631 (pt0) REVERT: C 540 PHE cc_start: 0.8677 (t80) cc_final: 0.8278 (t80) REVERT: E 195 ASP cc_start: 0.8902 (p0) cc_final: 0.8542 (p0) REVERT: E 210 MET cc_start: 0.8847 (mtm) cc_final: 0.8113 (mmp) REVERT: E 473 TYR cc_start: 0.8609 (m-80) cc_final: 0.8160 (m-80) REVERT: D 113 ASP cc_start: 0.8692 (t70) cc_final: 0.8449 (t0) REVERT: D 123 TYR cc_start: 0.9096 (m-80) cc_final: 0.8733 (m-80) REVERT: D 240 HIS cc_start: 0.8550 (m-70) cc_final: 0.8236 (t-170) REVERT: D 262 LYS cc_start: 0.8357 (tmtt) cc_final: 0.7932 (pttm) REVERT: D 365 ASP cc_start: 0.7964 (m-30) cc_final: 0.7720 (m-30) REVERT: D 467 ASP cc_start: 0.8272 (m-30) cc_final: 0.7811 (m-30) REVERT: D 496 MET cc_start: 0.8225 (mmp) cc_final: 0.7933 (mmp) REVERT: D 512 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7877 (mm-30) REVERT: F 287 ARG cc_start: 0.9276 (tmm160) cc_final: 0.9072 (ttp80) REVERT: F 332 PHE cc_start: 0.9215 (m-80) cc_final: 0.8955 (m-10) REVERT: F 335 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8528 (mmm160) REVERT: F 350 MET cc_start: 0.9396 (tmm) cc_final: 0.9066 (tmm) REVERT: F 354 MET cc_start: 0.8156 (mmp) cc_final: 0.7866 (mmp) REVERT: F 360 ASP cc_start: 0.9097 (p0) cc_final: 0.8668 (p0) REVERT: F 361 ASP cc_start: 0.8478 (p0) cc_final: 0.8090 (p0) REVERT: F 364 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8623 (mp0) REVERT: F 395 ASP cc_start: 0.8694 (m-30) cc_final: 0.8149 (m-30) REVERT: F 419 ASN cc_start: 0.9380 (m-40) cc_final: 0.9070 (m110) REVERT: 3 909 PHE cc_start: 0.7835 (m-80) cc_final: 0.7434 (m-80) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1608 time to fit residues: 115.1839 Evaluate side-chains 352 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 96 optimal weight: 0.0030 chunk 202 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 127 GLN ** 9 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN C 400 ASN E 58 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.102883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080064 restraints weight = 102823.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081060 restraints weight = 60956.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082123 restraints weight = 45332.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082715 restraints weight = 36401.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.082780 restraints weight = 32055.743| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25231 Z= 0.132 Angle : 0.655 11.117 34442 Z= 0.337 Chirality : 0.043 0.181 3957 Planarity : 0.004 0.066 4024 Dihedral : 17.086 129.756 4026 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.16), residues: 2738 helix: -0.52 (0.13), residues: 1485 sheet: -1.00 (0.35), residues: 220 loop : -1.39 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 218 TYR 0.019 0.001 TYR 9 291 PHE 0.025 0.001 PHE B 475 TRP 0.025 0.002 TRP F 378 HIS 0.013 0.001 HIS 9 204 Details of bonding type rmsd covalent geometry : bond 0.00294 (25231) covalent geometry : angle 0.65534 (34442) hydrogen bonds : bond 0.04100 ( 955) hydrogen bonds : angle 4.59551 ( 2696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 0.944 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: 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: 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: 9 201 ASN cc_start: 0.8628 (t0) cc_final: 0.7970 (t0) REVERT: 9 204 HIS cc_start: 0.7684 (m170) cc_final: 0.7115 (m170) REVERT: 9 222 LEU cc_start: 0.9564 (tp) cc_final: 0.9295 (tp) REVERT: 9 224 GLU cc_start: 0.8279 (tp30) cc_final: 0.7841 (tp30) REVERT: 9 244 GLU cc_start: 0.8071 (pt0) cc_final: 0.7612 (pt0) REVERT: 9 259 ILE cc_start: 0.8909 (mp) cc_final: 0.8575 (mp) REVERT: 9 261 MET cc_start: 0.8213 (mpp) cc_final: 0.7633 (mpp) REVERT: 9 323 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8221 (mmmt) REVERT: 9 434 ASP cc_start: 0.8750 (m-30) cc_final: 0.8360 (m-30) REVERT: 9 499 TYR cc_start: 0.9091 (m-10) cc_final: 0.8461 (m-80) REVERT: A 524 CYS cc_start: 0.9290 (m) cc_final: 0.8128 (m) REVERT: A 600 ASN cc_start: 0.8451 (p0) cc_final: 0.8221 (p0) REVERT: A 604 LEU cc_start: 0.8939 (tp) cc_final: 0.8304 (tp) REVERT: A 608 GLN cc_start: 0.9015 (mp10) cc_final: 0.8608 (mp10) REVERT: A 623 MET cc_start: 0.8240 (tpt) cc_final: 0.7885 (tmm) REVERT: A 843 MET cc_start: 0.8821 (mpp) cc_final: 0.8365 (mpp) REVERT: A 866 TRP cc_start: 0.8416 (t60) cc_final: 0.7952 (t60) REVERT: A 879 LEU cc_start: 0.9263 (mm) cc_final: 0.8891 (mm) REVERT: A 893 LYS cc_start: 0.9347 (tttt) cc_final: 0.9067 (ttmm) REVERT: A 902 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8862 (ttpp) REVERT: B 300 MET cc_start: 0.8713 (ptp) cc_final: 0.8114 (ptp) REVERT: B 377 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8691 (mmtm) REVERT: B 417 ASP cc_start: 0.7849 (t70) cc_final: 0.6010 (p0) REVERT: B 440 MET cc_start: 0.8517 (tmm) cc_final: 0.8113 (tmm) REVERT: B 458 HIS cc_start: 0.8375 (t-90) cc_final: 0.7969 (t70) REVERT: B 466 ASP cc_start: 0.8745 (p0) cc_final: 0.8474 (p0) REVERT: B 496 MET cc_start: 0.6187 (ppp) cc_final: 0.5519 (tmm) REVERT: B 498 MET cc_start: 0.4722 (mpp) cc_final: 0.4377 (pmm) REVERT: B 561 HIS cc_start: 0.9055 (m170) cc_final: 0.8333 (t-170) REVERT: B 563 CYS cc_start: 0.8869 (t) cc_final: 0.8649 (p) REVERT: B 611 LYS cc_start: 0.9463 (mmpt) cc_final: 0.9236 (mmmt) REVERT: C 106 PHE cc_start: 0.8667 (m-80) cc_final: 0.8439 (m-80) REVERT: C 204 ASN cc_start: 0.8817 (t0) cc_final: 0.8609 (t0) REVERT: C 206 LYS cc_start: 0.9155 (mmtp) cc_final: 0.8912 (mttp) REVERT: C 207 ASP cc_start: 0.8336 (t0) cc_final: 0.8123 (t0) REVERT: C 252 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7882 (ttp-110) REVERT: C 296 ASP cc_start: 0.9177 (p0) cc_final: 0.8827 (p0) REVERT: C 361 MET cc_start: 0.8860 (ptp) cc_final: 0.8535 (ptp) REVERT: C 423 ASN cc_start: 0.9547 (t0) cc_final: 0.8523 (t0) REVERT: C 498 LEU cc_start: 0.9313 (mm) cc_final: 0.8663 (mm) REVERT: C 523 GLN cc_start: 0.8044 (pt0) cc_final: 0.7521 (pt0) REVERT: C 540 PHE cc_start: 0.8597 (t80) cc_final: 0.8186 (t80) REVERT: C 585 MET cc_start: 0.7127 (ttt) cc_final: 0.5766 (tmm) REVERT: E 79 ARG cc_start: 0.8709 (ptp90) cc_final: 0.8329 (ptp-170) REVERT: E 153 ASN cc_start: 0.8736 (p0) cc_final: 0.8109 (p0) REVERT: E 195 ASP cc_start: 0.8841 (p0) cc_final: 0.8462 (p0) REVERT: E 210 MET cc_start: 0.8878 (mtm) cc_final: 0.8148 (mmp) REVERT: E 473 TYR cc_start: 0.8524 (m-80) cc_final: 0.8083 (m-80) REVERT: D 113 ASP cc_start: 0.8804 (t70) cc_final: 0.8555 (t0) REVERT: D 123 TYR cc_start: 0.8973 (m-80) cc_final: 0.8640 (m-80) REVERT: D 240 HIS cc_start: 0.8520 (m-70) cc_final: 0.8195 (t-170) REVERT: D 246 CYS cc_start: 0.7789 (p) cc_final: 0.7500 (p) REVERT: D 248 PHE cc_start: 0.8802 (m-80) cc_final: 0.8372 (m-80) REVERT: D 253 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8078 (mtmt) REVERT: D 338 LYS cc_start: 0.9331 (ptpt) cc_final: 0.8911 (pttm) REVERT: D 365 ASP cc_start: 0.7950 (m-30) cc_final: 0.7648 (m-30) REVERT: D 467 ASP cc_start: 0.8155 (m-30) cc_final: 0.7651 (m-30) REVERT: D 496 MET cc_start: 0.8028 (mmp) cc_final: 0.7787 (mmp) REVERT: D 512 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7866 (mm-30) REVERT: F 287 ARG cc_start: 0.9283 (tmm160) cc_final: 0.9074 (ttp80) REVERT: F 332 PHE cc_start: 0.9235 (m-80) cc_final: 0.8774 (m-80) REVERT: F 335 ARG cc_start: 0.8995 (mtt-85) cc_final: 0.8384 (mmm160) REVERT: F 336 ARG cc_start: 0.9168 (mtp-110) cc_final: 0.8795 (mtp85) REVERT: F 350 MET cc_start: 0.9392 (tmm) cc_final: 0.9055 (tmm) REVERT: F 354 MET cc_start: 0.8106 (mmp) cc_final: 0.7830 (mmp) REVERT: F 364 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8611 (mp0) REVERT: F 419 ASN cc_start: 0.9436 (m-40) cc_final: 0.9123 (m110) REVERT: 3 909 PHE cc_start: 0.7726 (m-80) cc_final: 0.7437 (m-80) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.1666 time to fit residues: 124.1829 Evaluate side-chains 375 residues out of total 2583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 127 GLN ** 9 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 295 GLN ** 9 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.102944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.079922 restraints weight = 103242.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081465 restraints weight = 60153.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.082491 restraints weight = 41891.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.082752 restraints weight = 35929.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082859 restraints weight = 31839.562| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25231 Z= 0.133 Angle : 0.656 10.820 34442 Z= 0.338 Chirality : 0.043 0.205 3957 Planarity : 0.004 0.085 4024 Dihedral : 17.028 126.927 4026 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.33 (0.16), residues: 2738 helix: -0.44 (0.13), residues: 1491 sheet: -0.98 (0.35), residues: 221 loop : -1.35 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 9 123 TYR 0.019 0.001 TYR 7 786 PHE 0.027 0.001 PHE B 475 TRP 0.044 0.002 TRP F 378 HIS 0.006 0.001 HIS A 777 Details of bonding type rmsd covalent geometry : bond 0.00294 (25231) covalent geometry : angle 0.65562 (34442) hydrogen bonds : bond 0.04084 ( 955) hydrogen bonds : angle 4.58639 ( 2696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.57 seconds wall clock time: 70 minutes 44.83 seconds (4244.83 seconds total)