Starting phenix.real_space_refine on Fri Dec 27 16:14:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxk_25500/12_2024/7sxk_25500.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 251 5.16 5 C 30579 2.51 5 N 8726 2.21 5 O 9381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48937 Number of models: 1 Model: "" Number of chains: 12 Chain: "b" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4325 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 17, 'TRANS': 550} Chain breaks: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 141 Chain: "a" Number of atoms: 4293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4293 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 540} Chain breaks: 2 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "l" Number of atoms: 4281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4281 Classifications: {'peptide': 555} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 17, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 221 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "k" Number of atoms: 4345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4345 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 17, 'TRANS': 547} Chain breaks: 2 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "j" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4405 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 17, 'TRANS': 560} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 133 Chain: "i" Number of atoms: 4322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4322 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 17, 'TRANS': 546} Chain breaks: 2 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 263 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 116 Chain: "h" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4108 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 17, 'TRANS': 541} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 397 Unresolved non-hydrogen angles: 499 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 15, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 236 Chain: "c" Number of atoms: 4377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4377 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 112 Chain: "d" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4358 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "e" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4323 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 17, 'TRANS': 544} Chain breaks: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 104 Chain: "f" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4077 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 15, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "g" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 1723 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 312} Link IDs: {'PTRANS': 7, 'TRANS': 340} Chain breaks: 4 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1175 Unresolved non-hydrogen angles: 1507 Unresolved non-hydrogen dihedrals: 974 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 8, 'PHE:plan': 13, 'GLU:plan': 25, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 703 Time building chain proxies: 24.81, per 1000 atoms: 0.51 Number of scatterers: 48937 At special positions: 0 Unit cell: (197.64, 194.4, 207.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 251 16.00 O 9381 8.00 N 8726 7.00 C 30579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS d 220 " - pdb=" SG CYS d 288 " distance=2.03 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: 9.56 Conformation dependent library (CDL) restraints added in 5.1 seconds 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12310 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 23 sheets defined 51.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'b' and resid 14 through 47 removed outlier: 3.923A pdb=" N PHE b 29 " --> pdb=" O ASP b 25 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER b 32 " --> pdb=" O ASP b 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS b 36 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN b 37 " --> pdb=" O GLU b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 81 Proline residue: b 74 - end of helix Processing helix chain 'b' and resid 95 through 110 removed outlier: 4.125A pdb=" N GLN b 99 " --> pdb=" O GLU b 95 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU b 101 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN b 102 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN b 108 " --> pdb=" O THR b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 132 removed outlier: 3.801A pdb=" N LYS b 132 " --> pdb=" O THR b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 200 through 202 No H-bonds generated for 'chain 'b' and resid 200 through 202' Processing helix chain 'b' and resid 226 through 233 Processing helix chain 'b' and resid 340 through 367 removed outlier: 6.534A pdb=" N ASP b 346 " --> pdb=" O ASP b 342 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE b 347 " --> pdb=" O LYS b 343 " (cutoff:3.500A) Processing helix chain 'b' and resid 377 through 387 removed outlier: 3.673A pdb=" N ASP b 381 " --> pdb=" O VAL b 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU b 382 " --> pdb=" O ASN b 378 " (cutoff:3.500A) Processing helix chain 'b' and resid 409 through 426 Processing helix chain 'b' and resid 445 through 455 removed outlier: 4.598A pdb=" N MET b 453 " --> pdb=" O VAL b 449 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 485 removed outlier: 4.756A pdb=" N LYS b 473 " --> pdb=" O GLU b 469 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG b 474 " --> pdb=" O THR b 470 " (cutoff:3.500A) Processing helix chain 'b' and resid 522 through 545 removed outlier: 3.545A pdb=" N ARG b 533 " --> pdb=" O LEU b 529 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP b 535 " --> pdb=" O LEU b 531 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU b 536 " --> pdb=" O MET b 532 " (cutoff:3.500A) Processing helix chain 'b' and resid 552 through 568 removed outlier: 3.708A pdb=" N LEU b 556 " --> pdb=" O SER b 552 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR b 557 " --> pdb=" O GLU b 553 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN b 558 " --> pdb=" O GLN b 554 " (cutoff:3.500A) Processing helix chain 'b' and resid 581 through 590 Processing helix chain 'b' and resid 590 through 595 Processing helix chain 'b' and resid 602 through 614 Processing helix chain 'b' and resid 619 through 639 removed outlier: 3.690A pdb=" N ALA b 623 " --> pdb=" O LYS b 619 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS b 626 " --> pdb=" O GLU b 622 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN b 627 " --> pdb=" O ALA b 623 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU b 639 " --> pdb=" O ALA b 635 " (cutoff:3.500A) Processing helix chain 'b' and resid 639 through 647 removed outlier: 4.212A pdb=" N ALA b 644 " --> pdb=" O LYS b 640 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL b 645 " --> pdb=" O LYS b 641 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 46 removed outlier: 3.765A pdb=" N ARG a 17 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER a 35 " --> pdb=" O SER a 31 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LYS a 36 " --> pdb=" O SER a 32 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 81 Proline residue: a 74 - end of helix Processing helix chain 'a' and resid 99 through 112 Processing helix chain 'a' and resid 118 through 131 Processing helix chain 'a' and resid 200 through 204 Processing helix chain 'a' and resid 226 through 232 Processing helix chain 'a' and resid 339 through 343 removed outlier: 3.537A pdb=" N ASP a 342 " --> pdb=" O SER a 339 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS a 343 " --> pdb=" O VAL a 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 339 through 343' Processing helix chain 'a' and resid 344 through 366 removed outlier: 3.609A pdb=" N ASN a 361 " --> pdb=" O ASN a 357 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 387 Processing helix chain 'a' and resid 410 through 426 Processing helix chain 'a' and resid 445 through 458 removed outlier: 4.021A pdb=" N GLU a 457 " --> pdb=" O MET a 453 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLN a 458 " --> pdb=" O THR a 454 " (cutoff:3.500A) Processing helix chain 'a' and resid 458 through 485 removed outlier: 3.755A pdb=" N LEU a 462 " --> pdb=" O GLN a 458 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS a 473 " --> pdb=" O GLU a 469 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG a 474 " --> pdb=" O THR a 470 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU a 475 " --> pdb=" O GLY a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 522 through 545 removed outlier: 4.418A pdb=" N GLU a 536 " --> pdb=" O MET a 532 " (cutoff:3.500A) Processing helix chain 'a' and resid 545 through 550 removed outlier: 4.601A pdb=" N VAL a 549 " --> pdb=" O GLY a 545 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU a 550 " --> pdb=" O GLY a 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 545 through 550' Processing helix chain 'a' and resid 555 through 568 removed outlier: 4.129A pdb=" N ASN a 566 " --> pdb=" O GLU a 562 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA a 567 " --> pdb=" O VAL a 563 " (cutoff:3.500A) Processing helix chain 'a' and resid 581 through 591 Processing helix chain 'a' and resid 592 through 597 removed outlier: 3.693A pdb=" N ALA a 596 " --> pdb=" O GLU a 592 " (cutoff:3.500A) Processing helix chain 'a' and resid 602 through 637 removed outlier: 3.846A pdb=" N ALA a 612 " --> pdb=" O ASP a 608 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA a 621 " --> pdb=" O LEU a 617 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU a 622 " --> pdb=" O ALA a 618 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS a 626 " --> pdb=" O GLU a 622 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN a 627 " --> pdb=" O ALA a 623 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 30 removed outlier: 4.298A pdb=" N ARG l 17 " --> pdb=" O GLU l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 46 removed outlier: 4.875A pdb=" N LYS l 36 " --> pdb=" O SER l 32 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN l 37 " --> pdb=" O GLU l 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE l 46 " --> pdb=" O LEU l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 64 through 81 Proline residue: l 74 - end of helix Processing helix chain 'l' and resid 99 through 112 Processing helix chain 'l' and resid 118 through 131 Processing helix chain 'l' and resid 200 through 204 removed outlier: 3.659A pdb=" N PHE l 204 " --> pdb=" O PRO l 201 " (cutoff:3.500A) Processing helix chain 'l' and resid 226 through 233 Processing helix chain 'l' and resid 340 through 343 Processing helix chain 'l' and resid 344 through 366 Processing helix chain 'l' and resid 377 through 387 Processing helix chain 'l' and resid 408 through 410 No H-bonds generated for 'chain 'l' and resid 408 through 410' Processing helix chain 'l' and resid 411 through 424 removed outlier: 4.162A pdb=" N LEU l 415 " --> pdb=" O VAL l 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP l 416 " --> pdb=" O TYR l 412 " (cutoff:3.500A) Processing helix chain 'l' and resid 445 through 458 Processing helix chain 'l' and resid 458 through 485 removed outlier: 4.000A pdb=" N LEU l 462 " --> pdb=" O GLN l 458 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS l 473 " --> pdb=" O GLU l 469 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG l 474 " --> pdb=" O THR l 470 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU l 475 " --> pdb=" O GLY l 471 " (cutoff:3.500A) Processing helix chain 'l' and resid 522 through 545 removed outlier: 4.106A pdb=" N GLU l 536 " --> pdb=" O MET l 532 " (cutoff:3.500A) Processing helix chain 'l' and resid 552 through 565 removed outlier: 3.530A pdb=" N LEU l 556 " --> pdb=" O SER l 552 " (cutoff:3.500A) Processing helix chain 'l' and resid 581 through 590 Processing helix chain 'l' and resid 592 through 596 Processing helix chain 'l' and resid 602 through 634 Processing helix chain 'k' and resid 14 through 46 removed outlier: 4.264A pdb=" N SER k 35 " --> pdb=" O SER k 31 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS k 36 " --> pdb=" O SER k 32 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN k 37 " --> pdb=" O GLU k 33 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE k 46 " --> pdb=" O LEU k 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 65 through 81 Proline residue: k 74 - end of helix Processing helix chain 'k' and resid 99 through 112 Processing helix chain 'k' and resid 117 through 130 removed outlier: 4.542A pdb=" N MET k 121 " --> pdb=" O GLY k 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE k 122 " --> pdb=" O PHE k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 200 through 204 Processing helix chain 'k' and resid 226 through 234 Processing helix chain 'k' and resid 340 through 366 removed outlier: 6.686A pdb=" N ASP k 346 " --> pdb=" O ASP k 342 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE k 347 " --> pdb=" O LYS k 343 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN k 366 " --> pdb=" O ILE k 362 " (cutoff:3.500A) Processing helix chain 'k' and resid 376 through 386 Processing helix chain 'k' and resid 410 through 426 removed outlier: 3.537A pdb=" N THR k 426 " --> pdb=" O ARG k 422 " (cutoff:3.500A) Processing helix chain 'k' and resid 445 through 458 removed outlier: 3.979A pdb=" N GLU k 457 " --> pdb=" O MET k 453 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN k 458 " --> pdb=" O THR k 454 " (cutoff:3.500A) Processing helix chain 'k' and resid 458 through 485 removed outlier: 4.013A pdb=" N LEU k 462 " --> pdb=" O GLN k 458 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS k 473 " --> pdb=" O GLU k 469 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ARG k 474 " --> pdb=" O THR k 470 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU k 475 " --> pdb=" O GLY k 471 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 533 Processing helix chain 'k' and resid 533 through 545 Processing helix chain 'k' and resid 552 through 565 removed outlier: 3.537A pdb=" N LEU k 556 " --> pdb=" O SER k 552 " (cutoff:3.500A) Processing helix chain 'k' and resid 581 through 591 Processing helix chain 'k' and resid 599 through 602 Processing helix chain 'k' and resid 603 through 644 removed outlier: 6.266A pdb=" N GLN k 627 " --> pdb=" O ALA k 623 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL k 628 " --> pdb=" O GLN k 624 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 46 removed outlier: 4.116A pdb=" N ARG j 17 " --> pdb=" O GLU j 13 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER j 35 " --> pdb=" O SER j 31 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS j 36 " --> pdb=" O SER j 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN j 37 " --> pdb=" O GLU j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 81 Proline residue: j 74 - end of helix Processing helix chain 'j' and resid 99 through 112 Processing helix chain 'j' and resid 116 through 131 removed outlier: 3.875A pdb=" N VAL j 120 " --> pdb=" O GLU j 116 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET j 121 " --> pdb=" O GLY j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 204 Processing helix chain 'j' and resid 212 through 216 removed outlier: 3.779A pdb=" N ALA j 216 " --> pdb=" O ILE j 213 " (cutoff:3.500A) Processing helix chain 'j' and resid 226 through 233 Processing helix chain 'j' and resid 340 through 366 removed outlier: 6.306A pdb=" N ASP j 346 " --> pdb=" O ASP j 342 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE j 347 " --> pdb=" O LYS j 343 " (cutoff:3.500A) Processing helix chain 'j' and resid 377 through 387 Processing helix chain 'j' and resid 409 through 425 removed outlier: 4.371A pdb=" N GLY j 413 " --> pdb=" O GLY j 409 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET j 414 " --> pdb=" O GLU j 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU j 415 " --> pdb=" O VAL j 411 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP j 416 " --> pdb=" O TYR j 412 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG j 417 " --> pdb=" O GLY j 413 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG j 425 " --> pdb=" O ASP j 421 " (cutoff:3.500A) Processing helix chain 'j' and resid 445 through 457 Processing helix chain 'j' and resid 458 through 483 removed outlier: 3.616A pdb=" N LEU j 462 " --> pdb=" O GLN j 458 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS j 473 " --> pdb=" O GLU j 469 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG j 474 " --> pdb=" O THR j 470 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU j 475 " --> pdb=" O GLY j 471 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA j 483 " --> pdb=" O LEU j 479 " (cutoff:3.500A) Processing helix chain 'j' and resid 522 through 533 Processing helix chain 'j' and resid 533 through 546 removed outlier: 3.659A pdb=" N GLY j 545 " --> pdb=" O VAL j 541 " (cutoff:3.500A) Processing helix chain 'j' and resid 552 through 568 removed outlier: 3.567A pdb=" N LEU j 556 " --> pdb=" O SER j 552 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN j 558 " --> pdb=" O GLN j 554 " (cutoff:3.500A) Processing helix chain 'j' and resid 581 through 592 Processing helix chain 'j' and resid 592 through 597 Processing helix chain 'j' and resid 603 through 619 removed outlier: 4.322A pdb=" N ALA j 607 " --> pdb=" O ILE j 603 " (cutoff:3.500A) Processing helix chain 'j' and resid 619 through 656 Processing helix chain 'i' and resid 13 through 33 removed outlier: 3.828A pdb=" N ARG i 17 " --> pdb=" O GLU i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 39 Processing helix chain 'i' and resid 40 through 46 Processing helix chain 'i' and resid 64 through 81 Proline residue: i 74 - end of helix Processing helix chain 'i' and resid 99 through 112 Processing helix chain 'i' and resid 118 through 131 Processing helix chain 'i' and resid 200 through 204 Processing helix chain 'i' and resid 226 through 233 Processing helix chain 'i' and resid 339 through 343 Processing helix chain 'i' and resid 344 through 362 removed outlier: 3.861A pdb=" N ASP i 360 " --> pdb=" O ARG i 356 " (cutoff:3.500A) Processing helix chain 'i' and resid 363 through 365 No H-bonds generated for 'chain 'i' and resid 363 through 365' Processing helix chain 'i' and resid 376 through 387 Processing helix chain 'i' and resid 413 through 427 removed outlier: 3.981A pdb=" N ARG i 417 " --> pdb=" O GLY i 413 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU i 418 " --> pdb=" O MET i 414 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR i 426 " --> pdb=" O ARG i 422 " (cutoff:3.500A) Processing helix chain 'i' and resid 429 through 433 Processing helix chain 'i' and resid 445 through 458 removed outlier: 3.663A pdb=" N VAL i 449 " --> pdb=" O ALA i 445 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN i 451 " --> pdb=" O MET i 447 " (cutoff:3.500A) Processing helix chain 'i' and resid 458 through 485 removed outlier: 4.293A pdb=" N LEU i 462 " --> pdb=" O GLN i 458 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS i 473 " --> pdb=" O GLU i 469 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG i 474 " --> pdb=" O THR i 470 " (cutoff:3.500A) Processing helix chain 'i' and resid 522 through 534 Processing helix chain 'i' and resid 537 through 544 removed outlier: 4.056A pdb=" N VAL i 541 " --> pdb=" O MET i 537 " (cutoff:3.500A) Processing helix chain 'i' and resid 552 through 568 removed outlier: 3.942A pdb=" N LEU i 556 " --> pdb=" O SER i 552 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU i 562 " --> pdb=" O ASN i 558 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL i 563 " --> pdb=" O ILE i 559 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA i 567 " --> pdb=" O VAL i 563 " (cutoff:3.500A) Processing helix chain 'i' and resid 581 through 597 removed outlier: 3.560A pdb=" N ARG i 591 " --> pdb=" O ALA i 587 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU i 592 " --> pdb=" O LYS i 588 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU i 595 " --> pdb=" O ARG i 591 " (cutoff:3.500A) Processing helix chain 'i' and resid 597 through 643 removed outlier: 4.063A pdb=" N GLN i 606 " --> pdb=" O ASP i 602 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA i 607 " --> pdb=" O ILE i 603 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU i 622 " --> pdb=" O ALA i 618 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA i 623 " --> pdb=" O LYS i 619 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 29 removed outlier: 3.617A pdb=" N ARG h 17 " --> pdb=" O GLU h 13 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 46 removed outlier: 4.371A pdb=" N SER h 35 " --> pdb=" O SER h 31 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS h 36 " --> pdb=" O SER h 32 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN h 37 " --> pdb=" O GLU h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 81 removed outlier: 3.542A pdb=" N GLU h 67 " --> pdb=" O ARG h 63 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR h 68 " --> pdb=" O ASP h 64 " (cutoff:3.500A) Proline residue: h 74 - end of helix Processing helix chain 'h' and resid 99 through 112 removed outlier: 3.738A pdb=" N GLU h 103 " --> pdb=" O GLN h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 118 through 129 removed outlier: 4.178A pdb=" N PHE h 125 " --> pdb=" O MET h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 200 through 204 removed outlier: 3.570A pdb=" N PHE h 204 " --> pdb=" O PRO h 201 " (cutoff:3.500A) Processing helix chain 'h' and resid 226 through 234 Processing helix chain 'h' and resid 340 through 367 removed outlier: 5.833A pdb=" N ASP h 346 " --> pdb=" O ASP h 342 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE h 347 " --> pdb=" O LYS h 343 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE h 350 " --> pdb=" O ASP h 346 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG h 356 " --> pdb=" O SER h 352 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE h 358 " --> pdb=" O LEU h 354 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N MET h 359 " --> pdb=" O MET h 355 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN h 366 " --> pdb=" O ILE h 362 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 387 Processing helix chain 'h' and resid 409 through 422 Processing helix chain 'h' and resid 423 through 426 Processing helix chain 'h' and resid 450 through 458 removed outlier: 3.720A pdb=" N GLN h 458 " --> pdb=" O THR h 454 " (cutoff:3.500A) Processing helix chain 'h' and resid 458 through 485 removed outlier: 4.072A pdb=" N VAL h 472 " --> pdb=" O ALA h 468 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS h 473 " --> pdb=" O GLU h 469 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG h 474 " --> pdb=" O THR h 470 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU h 478 " --> pdb=" O ARG h 474 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS h 485 " --> pdb=" O ASP h 481 " (cutoff:3.500A) Processing helix chain 'h' and resid 522 through 544 removed outlier: 4.592A pdb=" N TRP h 535 " --> pdb=" O LEU h 531 " (cutoff:3.500A) Processing helix chain 'h' and resid 552 through 568 removed outlier: 4.702A pdb=" N ASN h 558 " --> pdb=" O GLN h 554 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU h 562 " --> pdb=" O ASN h 558 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL h 563 " --> pdb=" O ILE h 559 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR h 564 " --> pdb=" O LEU h 560 " (cutoff:3.500A) Processing helix chain 'h' and resid 581 through 597 removed outlier: 3.640A pdb=" N LEU h 585 " --> pdb=" O SER h 581 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN h 597 " --> pdb=" O GLN h 593 " (cutoff:3.500A) Processing helix chain 'h' and resid 597 through 617 removed outlier: 3.982A pdb=" N ILE h 603 " --> pdb=" O LYS h 599 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN h 606 " --> pdb=" O ASP h 602 " (cutoff:3.500A) Processing helix chain 'h' and resid 619 through 622 removed outlier: 4.382A pdb=" N GLU h 622 " --> pdb=" O LYS h 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 619 through 622' Processing helix chain 'h' and resid 623 through 639 removed outlier: 4.002A pdb=" N GLU h 629 " --> pdb=" O MET h 625 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 33 removed outlier: 4.314A pdb=" N ARG c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE c 29 " --> pdb=" O ASP c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 47 removed outlier: 3.631A pdb=" N GLY c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 81 Proline residue: c 74 - end of helix Processing helix chain 'c' and resid 101 through 115 removed outlier: 4.423A pdb=" N VAL c 107 " --> pdb=" O GLU c 103 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN c 108 " --> pdb=" O THR c 104 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG c 113 " --> pdb=" O TYR c 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS c 114 " --> pdb=" O LEU c 110 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN c 115 " --> pdb=" O PHE c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 116 through 131 removed outlier: 4.001A pdb=" N VAL c 120 " --> pdb=" O GLU c 116 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET c 121 " --> pdb=" O GLY c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 200 through 204 Processing helix chain 'c' and resid 226 through 234 Processing helix chain 'c' and resid 339 through 343 removed outlier: 3.936A pdb=" N LYS c 343 " --> pdb=" O VAL c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 344 through 367 Processing helix chain 'c' and resid 377 through 386 Processing helix chain 'c' and resid 408 through 413 removed outlier: 4.225A pdb=" N TYR c 412 " --> pdb=" O SER c 408 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY c 413 " --> pdb=" O GLY c 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 408 through 413' Processing helix chain 'c' and resid 413 through 426 removed outlier: 3.627A pdb=" N ARG c 417 " --> pdb=" O GLY c 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 445 through 458 removed outlier: 3.672A pdb=" N VAL c 449 " --> pdb=" O ALA c 445 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU c 457 " --> pdb=" O MET c 453 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN c 458 " --> pdb=" O THR c 454 " (cutoff:3.500A) Processing helix chain 'c' and resid 458 through 485 removed outlier: 3.580A pdb=" N LEU c 462 " --> pdb=" O GLN c 458 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS c 473 " --> pdb=" O GLU c 469 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG c 474 " --> pdb=" O THR c 470 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU c 475 " --> pdb=" O GLY c 471 " (cutoff:3.500A) Processing helix chain 'c' and resid 522 through 545 removed outlier: 4.410A pdb=" N MET c 532 " --> pdb=" O MET c 528 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ARG c 533 " --> pdb=" O LEU c 529 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU c 536 " --> pdb=" O MET c 532 " (cutoff:3.500A) Processing helix chain 'c' and resid 552 through 568 Processing helix chain 'c' and resid 581 through 590 Processing helix chain 'c' and resid 592 through 597 removed outlier: 4.657A pdb=" N GLN c 597 " --> pdb=" O GLN c 593 " (cutoff:3.500A) Processing helix chain 'c' and resid 602 through 610 removed outlier: 4.514A pdb=" N ASP c 608 " --> pdb=" O LYS c 604 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 613 No H-bonds generated for 'chain 'c' and resid 611 through 613' Processing helix chain 'c' and resid 617 through 647 removed outlier: 3.674A pdb=" N ALA c 621 " --> pdb=" O LEU c 617 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN c 647 " --> pdb=" O GLU c 643 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 47 removed outlier: 3.530A pdb=" N ARG d 17 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE d 29 " --> pdb=" O ASP d 25 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER d 35 " --> pdb=" O SER d 31 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS d 36 " --> pdb=" O SER d 32 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE d 46 " --> pdb=" O LEU d 42 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY d 47 " --> pdb=" O LYS d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 81 Proline residue: d 74 - end of helix Processing helix chain 'd' and resid 99 through 112 Processing helix chain 'd' and resid 118 through 131 Processing helix chain 'd' and resid 200 through 204 Processing helix chain 'd' and resid 226 through 234 Processing helix chain 'd' and resid 340 through 365 removed outlier: 6.560A pdb=" N ASP d 346 " --> pdb=" O ASP d 342 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ILE d 347 " --> pdb=" O LYS d 343 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN d 361 " --> pdb=" O ASN d 357 " (cutoff:3.500A) Processing helix chain 'd' and resid 379 through 387 Processing helix chain 'd' and resid 410 through 426 Processing helix chain 'd' and resid 445 through 458 removed outlier: 3.862A pdb=" N GLU d 457 " --> pdb=" O MET d 453 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN d 458 " --> pdb=" O THR d 454 " (cutoff:3.500A) Processing helix chain 'd' and resid 458 through 485 removed outlier: 3.806A pdb=" N LEU d 462 " --> pdb=" O GLN d 458 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS d 473 " --> pdb=" O GLU d 469 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG d 474 " --> pdb=" O THR d 470 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU d 475 " --> pdb=" O GLY d 471 " (cutoff:3.500A) Processing helix chain 'd' and resid 512 through 516 removed outlier: 3.668A pdb=" N VAL d 515 " --> pdb=" O ASP d 512 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR d 516 " --> pdb=" O LEU d 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 512 through 516' Processing helix chain 'd' and resid 522 through 545 removed outlier: 3.803A pdb=" N TRP d 535 " --> pdb=" O LEU d 531 " (cutoff:3.500A) Processing helix chain 'd' and resid 552 through 568 removed outlier: 3.785A pdb=" N LEU d 556 " --> pdb=" O SER d 552 " (cutoff:3.500A) Processing helix chain 'd' and resid 581 through 590 Processing helix chain 'd' and resid 590 through 597 removed outlier: 3.734A pdb=" N GLN d 597 " --> pdb=" O GLN d 593 " (cutoff:3.500A) Processing helix chain 'd' and resid 598 through 602 removed outlier: 3.907A pdb=" N ASP d 602 " --> pdb=" O LYS d 599 " (cutoff:3.500A) Processing helix chain 'd' and resid 603 through 614 removed outlier: 3.896A pdb=" N SER d 614 " --> pdb=" O GLN d 610 " (cutoff:3.500A) Processing helix chain 'd' and resid 618 through 647 removed outlier: 3.534A pdb=" N GLU d 629 " --> pdb=" O MET d 625 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 46 removed outlier: 5.473A pdb=" N LYS e 36 " --> pdb=" O SER e 32 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN e 37 " --> pdb=" O GLU e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 81 removed outlier: 3.830A pdb=" N THR e 68 " --> pdb=" O ASP e 64 " (cutoff:3.500A) Proline residue: e 74 - end of helix Processing helix chain 'e' and resid 100 through 112 Processing helix chain 'e' and resid 118 through 130 Processing helix chain 'e' and resid 200 through 204 Processing helix chain 'e' and resid 212 through 216 removed outlier: 3.743A pdb=" N ASP e 215 " --> pdb=" O CYS e 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 226 through 234 Processing helix chain 'e' and resid 339 through 367 removed outlier: 6.507A pdb=" N ASP e 346 " --> pdb=" O ASP e 342 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE e 347 " --> pdb=" O LYS e 343 " (cutoff:3.500A) Processing helix chain 'e' and resid 377 through 387 Processing helix chain 'e' and resid 408 through 410 No H-bonds generated for 'chain 'e' and resid 408 through 410' Processing helix chain 'e' and resid 411 through 425 removed outlier: 3.694A pdb=" N LEU e 415 " --> pdb=" O VAL e 411 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP e 416 " --> pdb=" O TYR e 412 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG e 417 " --> pdb=" O GLY e 413 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG e 425 " --> pdb=" O ASP e 421 " (cutoff:3.500A) Processing helix chain 'e' and resid 445 through 458 removed outlier: 3.930A pdb=" N VAL e 449 " --> pdb=" O ALA e 445 " (cutoff:3.500A) Processing helix chain 'e' and resid 458 through 472 removed outlier: 3.607A pdb=" N LEU e 462 " --> pdb=" O GLN e 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 472 through 485 removed outlier: 3.884A pdb=" N LEU e 478 " --> pdb=" O ARG e 474 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS e 485 " --> pdb=" O ASP e 481 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 516 removed outlier: 3.873A pdb=" N VAL e 515 " --> pdb=" O ASP e 512 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR e 516 " --> pdb=" O LEU e 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 512 through 516' Processing helix chain 'e' and resid 522 through 531 Processing helix chain 'e' and resid 534 through 545 Processing helix chain 'e' and resid 552 through 568 removed outlier: 4.052A pdb=" N ASN e 558 " --> pdb=" O GLN e 554 " (cutoff:3.500A) Processing helix chain 'e' and resid 581 through 590 Processing helix chain 'e' and resid 590 through 595 Processing helix chain 'e' and resid 602 through 612 Processing helix chain 'e' and resid 617 through 641 removed outlier: 3.569A pdb=" N MET e 625 " --> pdb=" O ALA e 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 32 removed outlier: 4.220A pdb=" N ARG f 17 " --> pdb=" O GLU f 13 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN f 24 " --> pdb=" O ASP f 20 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP f 25 " --> pdb=" O GLN f 21 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER f 32 " --> pdb=" O ASP f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 46 Processing helix chain 'f' and resid 64 through 81 Proline residue: f 74 - end of helix Processing helix chain 'f' and resid 99 through 112 removed outlier: 3.861A pdb=" N THR f 104 " --> pdb=" O ALA f 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 118 through 123 Processing helix chain 'f' and resid 124 through 130 Processing helix chain 'f' and resid 200 through 202 No H-bonds generated for 'chain 'f' and resid 200 through 202' Processing helix chain 'f' and resid 212 through 216 removed outlier: 3.874A pdb=" N ALA f 216 " --> pdb=" O ILE f 213 " (cutoff:3.500A) Processing helix chain 'f' and resid 226 through 233 Processing helix chain 'f' and resid 339 through 364 removed outlier: 3.515A pdb=" N LYS f 343 " --> pdb=" O SER f 339 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP f 346 " --> pdb=" O ASP f 342 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE f 347 " --> pdb=" O LYS f 343 " (cutoff:3.500A) Processing helix chain 'f' and resid 365 through 367 No H-bonds generated for 'chain 'f' and resid 365 through 367' Processing helix chain 'f' and resid 376 through 387 removed outlier: 3.825A pdb=" N GLU f 380 " --> pdb=" O GLN f 376 " (cutoff:3.500A) Processing helix chain 'f' and resid 409 through 427 removed outlier: 3.719A pdb=" N GLY f 413 " --> pdb=" O GLY f 409 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU f 415 " --> pdb=" O VAL f 411 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP f 416 " --> pdb=" O TYR f 412 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG f 417 " --> pdb=" O GLY f 413 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG f 425 " --> pdb=" O ASP f 421 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR f 426 " --> pdb=" O ARG f 422 " (cutoff:3.500A) Processing helix chain 'f' and resid 429 through 433 removed outlier: 3.794A pdb=" N ARG f 433 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 445 through 458 removed outlier: 4.322A pdb=" N VAL f 449 " --> pdb=" O ALA f 445 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN f 451 " --> pdb=" O MET f 447 " (cutoff:3.500A) Processing helix chain 'f' and resid 458 through 485 removed outlier: 3.852A pdb=" N LEU f 462 " --> pdb=" O GLN f 458 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LYS f 473 " --> pdb=" O GLU f 469 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG f 474 " --> pdb=" O THR f 470 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU f 475 " --> pdb=" O GLY f 471 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP f 481 " --> pdb=" O GLN f 477 " (cutoff:3.500A) Processing helix chain 'f' and resid 512 through 516 removed outlier: 3.747A pdb=" N VAL f 515 " --> pdb=" O ASP f 512 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR f 516 " --> pdb=" O LEU f 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 512 through 516' Processing helix chain 'f' and resid 522 through 534 Processing helix chain 'f' and resid 534 through 542 removed outlier: 3.677A pdb=" N GLN f 539 " --> pdb=" O TRP f 535 " (cutoff:3.500A) Processing helix chain 'f' and resid 552 through 567 Processing helix chain 'f' and resid 584 through 596 Processing helix chain 'g' and resid 13 through 27 removed outlier: 3.568A pdb=" N ARG g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU g 27 " --> pdb=" O VAL g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 38 Processing helix chain 'g' and resid 64 through 73 removed outlier: 4.914A pdb=" N ASP g 70 " --> pdb=" O GLN g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 81 Processing helix chain 'g' and resid 101 through 112 removed outlier: 3.706A pdb=" N TYR g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU g 110 " --> pdb=" O TYR g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 132 removed outlier: 3.915A pdb=" N TRP g 124 " --> pdb=" O VAL g 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE g 125 " --> pdb=" O MET g 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 200 through 204 Processing helix chain 'g' and resid 344 through 351 removed outlier: 3.737A pdb=" N GLU g 349 " --> pdb=" O ARG g 345 " (cutoff:3.500A) Processing helix chain 'g' and resid 414 through 419 Processing helix chain 'g' and resid 420 through 422 No H-bonds generated for 'chain 'g' and resid 420 through 422' Processing helix chain 'g' and resid 434 through 462 removed outlier: 4.151A pdb=" N VAL g 449 " --> pdb=" O ALA g 445 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASN g 450 " --> pdb=" O ALA g 446 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN g 451 " --> pdb=" O MET g 447 " (cutoff:3.500A) Processing helix chain 'g' and resid 505 through 514 removed outlier: 4.073A pdb=" N SER g 511 " --> pdb=" O TRP g 507 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP g 512 " --> pdb=" O ARG g 508 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR g 514 " --> pdb=" O ARG g 510 " (cutoff:3.500A) Processing helix chain 'g' and resid 522 through 524 No H-bonds generated for 'chain 'g' and resid 522 through 524' Processing helix chain 'g' and resid 525 through 532 removed outlier: 4.056A pdb=" N LEU g 529 " --> pdb=" O ASP g 525 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS g 530 " --> pdb=" O GLN g 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 136 through 143 Processing sheet with id=AA2, first strand: chain 'b' and resid 204 through 205 removed outlier: 3.803A pdb=" N CYS b 220 " --> pdb=" O LEU b 205 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA b 285 " --> pdb=" O GLU b 223 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR b 290 " --> pdb=" O ARG b 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 137 through 143 Processing sheet with id=AA4, first strand: chain 'a' and resid 218 through 223 Processing sheet with id=AA5, first strand: chain 'l' and resid 136 through 143 Processing sheet with id=AA6, first strand: chain 'l' and resid 219 through 221 removed outlier: 3.613A pdb=" N THR l 290 " --> pdb=" O ARG l 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'k' and resid 138 through 143 Processing sheet with id=AA8, first strand: chain 'k' and resid 218 through 223 removed outlier: 3.618A pdb=" N THR k 290 " --> pdb=" O ARG k 303 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG k 304 " --> pdb=" O GLU k 316 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER k 314 " --> pdb=" O LEU k 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 137 through 142 Processing sheet with id=AB1, first strand: chain 'j' and resid 218 through 223 removed outlier: 3.509A pdb=" N ALA j 285 " --> pdb=" O GLU j 223 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER j 314 " --> pdb=" O LEU j 306 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'i' and resid 136 through 143 Processing sheet with id=AB3, first strand: chain 'i' and resid 218 through 223 removed outlier: 3.654A pdb=" N LEU i 302 " --> pdb=" O TRP i 318 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU i 316 " --> pdb=" O ARG i 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 136 through 143 removed outlier: 4.319A pdb=" N TYR h 139 " --> pdb=" O LYS h 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS h 195 " --> pdb=" O TYR h 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'c' and resid 138 through 143 Processing sheet with id=AB7, first strand: chain 'c' and resid 218 through 223 removed outlier: 3.636A pdb=" N GLU c 316 " --> pdb=" O ARG c 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 136 through 141 Processing sheet with id=AB9, first strand: chain 'd' and resid 205 through 206 removed outlier: 3.777A pdb=" N THR d 290 " --> pdb=" O ARG d 303 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 136 through 142 Processing sheet with id=AC2, first strand: chain 'e' and resid 218 through 223 removed outlier: 3.851A pdb=" N GLU e 316 " --> pdb=" O ARG e 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 137 through 143 Processing sheet with id=AC4, first strand: chain 'f' and resid 204 through 206 removed outlier: 3.708A pdb=" N SER f 286 " --> pdb=" O TYR f 307 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'g' and resid 137 through 138 2347 hydrogen bonds defined for protein. 6846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.14 Time building geometry restraints manager: 11.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16951 1.34 - 1.46: 10189 1.46 - 1.58: 22132 1.58 - 1.71: 0 1.71 - 1.83: 447 Bond restraints: 49719 Sorted by residual: bond pdb=" N ILE j 632 " pdb=" CA ILE j 632 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.41e+00 bond pdb=" N VAL j 645 " pdb=" CA VAL j 645 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.29e+00 bond pdb=" N ILE j 637 " pdb=" CA ILE j 637 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.29e+00 bond pdb=" N VAL j 628 " pdb=" CA VAL j 628 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.23e+00 bond pdb=" N GLN j 620 " pdb=" CA GLN j 620 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.21e-02 6.83e+03 6.73e+00 ... (remaining 49714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 65866 2.17 - 4.33: 1294 4.33 - 6.50: 184 6.50 - 8.67: 36 8.67 - 10.84: 3 Bond angle restraints: 67383 Sorted by residual: angle pdb=" N VAL i 294 " pdb=" CA VAL i 294 " pdb=" C VAL i 294 " ideal model delta sigma weight residual 113.42 107.26 6.16 1.17e+00 7.31e-01 2.77e+01 angle pdb=" C MET l 131 " pdb=" N LYS l 132 " pdb=" CA LYS l 132 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C PHE l 575 " pdb=" N TRP l 576 " pdb=" CA TRP l 576 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" N GLN b 376 " pdb=" CA GLN b 376 " pdb=" C GLN b 376 " ideal model delta sigma weight residual 108.19 113.22 -5.03 1.29e+00 6.01e-01 1.52e+01 angle pdb=" N GLU l 601 " pdb=" CA GLU l 601 " pdb=" C GLU l 601 " ideal model delta sigma weight residual 113.40 107.90 5.50 1.47e+00 4.63e-01 1.40e+01 ... (remaining 67378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 26850 17.85 - 35.70: 2806 35.70 - 53.55: 431 53.55 - 71.40: 65 71.40 - 89.25: 46 Dihedral angle restraints: 30198 sinusoidal: 11230 harmonic: 18968 Sorted by residual: dihedral pdb=" CA SER c 448 " pdb=" C SER c 448 " pdb=" N VAL c 449 " pdb=" CA VAL c 449 " ideal model delta harmonic sigma weight residual 180.00 -118.83 -61.17 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA SER d 448 " pdb=" C SER d 448 " pdb=" N VAL d 449 " pdb=" CA VAL d 449 " ideal model delta harmonic sigma weight residual -180.00 -122.88 -57.12 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA SER e 448 " pdb=" C SER e 448 " pdb=" N VAL e 449 " pdb=" CA VAL e 449 " ideal model delta harmonic sigma weight residual -180.00 -123.11 -56.89 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 30195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 5360 0.042 - 0.085: 1659 0.085 - 0.127: 468 0.127 - 0.170: 75 0.170 - 0.212: 15 Chirality restraints: 7577 Sorted by residual: chirality pdb=" CB VAL c 377 " pdb=" CA VAL c 377 " pdb=" CG1 VAL c 377 " pdb=" CG2 VAL c 377 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA TRP l 576 " pdb=" N TRP l 576 " pdb=" C TRP l 576 " pdb=" CB TRP l 576 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL j 628 " pdb=" N VAL j 628 " pdb=" C VAL j 628 " pdb=" CB VAL j 628 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 7574 not shown) Planarity restraints: 8946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 124 " 0.030 2.00e-02 2.50e+03 2.31e-02 1.34e+01 pdb=" CG TRP a 124 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP a 124 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP a 124 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 124 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP a 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 124 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 124 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 124 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS k 599 " 0.057 5.00e-02 4.00e+02 8.75e-02 1.22e+01 pdb=" N PRO k 600 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO k 600 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO k 600 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP j 571 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO j 572 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO j 572 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO j 572 " 0.040 5.00e-02 4.00e+02 ... (remaining 8943 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1448 2.70 - 3.25: 52305 3.25 - 3.80: 75680 3.80 - 4.35: 95789 4.35 - 4.90: 152446 Nonbonded interactions: 377668 Sorted by model distance: nonbonded pdb=" OG1 THR i 226 " pdb=" OD1 ASN i 280 " model vdw 2.147 3.040 nonbonded pdb=" O VAL l 549 " pdb=" ND2 ASN k 578 " model vdw 2.168 3.120 nonbonded pdb=" NE1 TRP i 71 " pdb=" O THR i 432 " model vdw 2.168 3.120 nonbonded pdb=" OH TYR c 139 " pdb=" OE2 GLU c 287 " model vdw 2.171 3.040 nonbonded pdb=" O ASP a 238 " pdb=" OH TYR a 311 " model vdw 2.174 3.040 ... (remaining 377663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'a' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 368 through 400 and (name N or name CA or \ name C or name O or name CB )) or resid 401 through 597)) selection = (chain 'b' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 28 or (resid 29 through 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 through 44 or (res \ id 45 and (name N or name CA or name C or name O or name CB )) or resid 46 throu \ gh 47 or (resid 48 through 50 and (name N or name CA or name C or name O or name \ CB )) or resid 51 or (resid 52 through 55 and (name N or name CA or name C or n \ ame O or name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA o \ r name C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name \ N or name CA or name C or name O or name CB )) or resid 146 through 223 or (res \ id 224 through 225 and (name N or name CA or name C or name O or name CB )) or r \ esid 226 through 229 or (resid 230 and (name N or name CA or name C or name O or \ name CB )) or resid 231 or (resid 232 through 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 or (resid 235 through 239 and (name N o \ r name CA or name C or name O or name CB )) or (resid 278 through 282 and (name \ N or name CA or name C or name O or name CB )) or resid 283 through 293 or (resi \ d 294 through 295 and (name N or name CA or name C or name O or name CB )) or re \ sid 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 or (resid 299 through 301 and (name N or name CA or name C or name O \ or name CB )) or resid 302 through 309 or (resid 310 through 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 340 or (resid 34 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 342 through \ 397 or (resid 398 through 400 and (name N or name CA or name C or name O or name \ CB )) or resid 401 through 507 or (resid 508 and (name N or name CA or name C o \ r name O or name CB )) or resid 509 through 597)) selection = (chain 'c' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 or (resid 369 through 374 and (name N o \ r name CA or name C or name O or name CB )) or (resid 375 through 388 and (name \ N or name CA or name C or name O or name CB )) or (resid 389 through 400 and (na \ me N or name CA or name C or name O or name CB )) or resid 401 through 507 or (r \ esid 508 and (name N or name CA or name C or name O or name CB )) or resid 509 t \ hrough 597)) selection = (chain 'd' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 368 through 400 and (name N or name CA or \ name C or name O or name CB )) or resid 401 through 507 or (resid 508 and (name \ N or name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'e' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 368 through 400 and (name N or name CA or \ name C or name O or name CB )) or resid 401 through 507 or (resid 508 and (name \ N or name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'f' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or resid 278 th \ rough 293 or (resid 294 through 295 and (name N or name CA or name C or name O o \ r name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name CA o \ r name C or name O or name CB )) or resid 302 through 309 or (resid 310 through \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throug \ h 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) or \ resid 342 through 365 or (resid 366 through 367 and (name N or name CA or name C \ or name O or name CB )) or (resid 368 through 400 and (name N or name CA or nam \ e C or name O or name CB )) or resid 401 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'h' and (resid 9 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 148 or (resid 185 thro \ ugh 186 and (name N or name CA or name C or name O or name CB )) or resid 187 th \ rough 279 or (resid 280 through 282 and (name N or name CA or name C or name O o \ r name CB )) or resid 283 through 507 or (resid 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 597)) selection = (chain 'i' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'j' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'k' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 365 or (resid 366 through 367 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 368 through 400 and (name N or name CA or \ name C or name O or name CB )) or resid 401 through 507 or (resid 508 and (name \ N or name CA or name C or name O or name CB )) or resid 509 through 597)) selection = (chain 'l' and ((resid 9 through 14 and (name N or name CA or name C or name O o \ r name CB )) or resid 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 or (resid 18 and (name N or name CA or name C or name \ O or name CB )) or resid 19 or (resid 20 and (name N or name CA or name C or na \ me O or name CB )) or resid 21 through 28 or (resid 29 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 through 44 or (resid 45 a \ nd (name N or name CA or name C or name O or name CB )) or resid 46 through 47 o \ r (resid 48 through 50 and (name N or name CA or name C or name O or name CB )) \ or resid 51 or (resid 52 through 55 and (name N or name CA or name C or name O o \ r name CB )) or resid 56 or (resid 57 through 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 144 or (resid 145 and (name N or n \ ame CA or name C or name O or name CB )) or resid 146 through 147 or (resid 148 \ through 186 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 7 through 223 or (resid 224 through 225 and (name N or name CA or name C or name \ O or name CB )) or resid 226 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 or (resid 232 through 233 and (nam \ e N or name CA or name C or name O or name CB )) or resid 234 or (resid 235 thro \ ugh 239 and (name N or name CA or name C or name O or name CB )) or (resid 278 t \ hrough 282 and (name N or name CA or name C or name O or name CB )) or resid 283 \ through 293 or (resid 294 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 or (resid 299 through 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 309 or (resid 310 throu \ gh 312 and (name N or name CA or name C or name O or name CB )) or resid 313 thr \ ough 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 507 or (resid 508 and (name N or name CA or \ name C or name O or name CB )) or resid 509 through 597)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.380 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 81.090 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 : 0.003 0.067 49719 Z= 0.204 Angle : 0.723 10.837 67383 Z= 0.392 Chirality : 0.045 0.212 7577 Planarity : 0.004 0.087 8946 Dihedral : 14.869 89.255 17885 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 18.67 % Favored : 81.02 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 6437 helix: 0.18 (0.10), residues: 2876 sheet: -1.81 (0.23), residues: 533 loop : -4.07 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP a 124 HIS 0.015 0.001 HIS i 482 PHE 0.020 0.002 PHE f 476 TYR 0.030 0.002 TYR l 341 ARG 0.005 0.000 ARG a 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 4.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 421 ASP cc_start: 0.7467 (m-30) cc_final: 0.7074 (m-30) REVERT: b 524 LYS cc_start: 0.8508 (mttp) cc_final: 0.7893 (mtpt) REVERT: l 537 MET cc_start: 0.7532 (mmt) cc_final: 0.7189 (mmt) REVERT: k 77 MET cc_start: 0.8147 (mmp) cc_final: 0.7938 (mmp) REVERT: j 359 MET cc_start: 0.7986 (ptm) cc_final: 0.7569 (tmm) REVERT: i 338 MET cc_start: 0.5637 (ppp) cc_final: 0.5351 (ppp) REVERT: c 532 MET cc_start: 0.8026 (mtp) cc_final: 0.7789 (mtp) REVERT: c 537 MET cc_start: 0.8397 (mtp) cc_final: 0.8167 (mtp) REVERT: e 466 MET cc_start: 0.8572 (pmm) cc_final: 0.8217 (pmm) REVERT: e 557 TYR cc_start: 0.6077 (m-10) cc_final: 0.5844 (m-80) REVERT: f 77 MET cc_start: 0.7787 (mmt) cc_final: 0.7313 (mmm) REVERT: f 535 TRP cc_start: -0.0514 (m100) cc_final: -0.0811 (m100) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.4664 time to fit residues: 261.5731 Evaluate side-chains 297 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 542 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 328 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 503 optimal weight: 30.0000 chunk 195 optimal weight: 50.0000 chunk 306 optimal weight: 9.9990 chunk 375 optimal weight: 10.0000 chunk 583 optimal weight: 30.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 451 GLN b 459 GLN a 437 GLN ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 108 ASN k 221 HIS k 333 HIS ** k 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 108 ASN ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 489 GLN ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 437 GLN e 487 GLN ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 49719 Z= 0.251 Angle : 0.733 10.051 67383 Z= 0.386 Chirality : 0.045 0.214 7577 Planarity : 0.005 0.087 8946 Dihedral : 6.494 60.364 7017 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.68 % Favored : 80.01 % Rotamer: Outliers : 0.49 % Allowed : 8.30 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 6437 helix: -0.01 (0.10), residues: 2953 sheet: -1.72 (0.24), residues: 516 loop : -4.14 (0.10), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP j 124 HIS 0.020 0.001 HIS i 482 PHE 0.016 0.002 PHE l 575 TYR 0.037 0.002 TYR l 341 ARG 0.005 0.001 ARG i 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 421 ASP cc_start: 0.7539 (m-30) cc_final: 0.7253 (m-30) REVERT: a 537 MET cc_start: 0.8406 (mmm) cc_final: 0.8129 (mtp) REVERT: k 77 MET cc_start: 0.8355 (mmp) cc_final: 0.8114 (mmp) REVERT: k 108 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8404 (t0) REVERT: k 535 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.6875 (t60) REVERT: j 359 MET cc_start: 0.8054 (ptm) cc_final: 0.7684 (tmm) REVERT: i 73 MET cc_start: 0.8322 (mmt) cc_final: 0.8049 (mmm) REVERT: h 130 MET cc_start: 0.6789 (mpp) cc_final: 0.5637 (mtp) REVERT: c 537 MET cc_start: 0.8451 (mtp) cc_final: 0.8221 (mtp) REVERT: f 121 MET cc_start: 0.7927 (mmp) cc_final: 0.7190 (ptm) outliers start: 23 outliers final: 8 residues processed: 325 average time/residue: 0.4539 time to fit residues: 253.5169 Evaluate side-chains 308 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 298 time to evaluate : 4.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain a residue 124 TRP Chi-restraints excluded: chain a residue 570 LYS Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain k residue 535 TRP Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain d residue 492 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 324 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 485 optimal weight: 7.9990 chunk 397 optimal weight: 0.0570 chunk 161 optimal weight: 4.9990 chunk 584 optimal weight: 40.0000 chunk 631 optimal weight: 50.0000 chunk 520 optimal weight: 20.0000 chunk 580 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 469 optimal weight: 30.0000 overall best weight: 3.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 459 GLN ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 506 ASN k 487 GLN k 506 ASN ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 539 GLN h 477 GLN ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 361 ASN ** c 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 450 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 578 ASN ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 49719 Z= 0.193 Angle : 0.687 9.386 67383 Z= 0.362 Chirality : 0.043 0.195 7577 Planarity : 0.004 0.083 8946 Dihedral : 6.320 61.125 7017 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.41 % Favored : 81.30 % Rotamer: Outliers : 0.90 % Allowed : 11.38 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 6437 helix: 0.11 (0.10), residues: 2941 sheet: -1.65 (0.24), residues: 507 loop : -4.10 (0.10), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP j 124 HIS 0.019 0.001 HIS i 482 PHE 0.017 0.002 PHE d 575 TYR 0.020 0.001 TYR l 341 ARG 0.007 0.000 ARG k 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 421 ASP cc_start: 0.7491 (m-30) cc_final: 0.7224 (m-30) REVERT: l 537 MET cc_start: 0.7772 (mmt) cc_final: 0.7179 (mmt) REVERT: k 77 MET cc_start: 0.8369 (mmp) cc_final: 0.8085 (mmp) REVERT: k 535 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.7350 (t60) REVERT: j 359 MET cc_start: 0.8038 (ptm) cc_final: 0.7659 (tmm) REVERT: j 528 MET cc_start: 0.7959 (mmp) cc_final: 0.7550 (mmm) REVERT: j 532 MET cc_start: 0.7483 (mtt) cc_final: 0.7221 (mtm) REVERT: j 537 MET cc_start: 0.7609 (mpp) cc_final: 0.7384 (ptt) REVERT: i 73 MET cc_start: 0.8361 (mmt) cc_final: 0.8022 (mmm) REVERT: i 338 MET cc_start: 0.5863 (ppp) cc_final: 0.5534 (ppp) REVERT: c 537 MET cc_start: 0.8496 (mtp) cc_final: 0.8276 (mtp) REVERT: d 294 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7548 (t) REVERT: e 453 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4103 (tmm) REVERT: e 466 MET cc_start: 0.8746 (pmm) cc_final: 0.8307 (pmm) REVERT: e 482 HIS cc_start: 0.7013 (m-70) cc_final: 0.6805 (m-70) REVERT: e 532 MET cc_start: 0.6754 (ttt) cc_final: 0.6359 (ttp) REVERT: f 121 MET cc_start: 0.8034 (mmp) cc_final: 0.7300 (ptm) REVERT: f 447 MET cc_start: 0.1955 (OUTLIER) cc_final: 0.1505 (mtm) outliers start: 42 outliers final: 15 residues processed: 342 average time/residue: 0.4691 time to fit residues: 273.3444 Evaluate side-chains 319 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 300 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 124 TRP Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain k residue 535 TRP Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 453 MET Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 294 VAL Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 437 GLN Chi-restraints excluded: chain f residue 447 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 577 optimal weight: 0.1980 chunk 439 optimal weight: 20.0000 chunk 303 optimal weight: 50.0000 chunk 64 optimal weight: 0.6980 chunk 279 optimal weight: 5.9990 chunk 392 optimal weight: 40.0000 chunk 587 optimal weight: 30.0000 chunk 621 optimal weight: 50.0000 chunk 306 optimal weight: 5.9990 chunk 556 optimal weight: 7.9990 chunk 167 optimal weight: 40.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 ASN j 203 ASN ** j 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 482 HIS d 555 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 527 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 49719 Z= 0.191 Angle : 0.674 9.281 67383 Z= 0.354 Chirality : 0.043 0.193 7577 Planarity : 0.004 0.079 8946 Dihedral : 6.227 61.029 7017 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 19.02 % Favored : 80.71 % Rotamer: Outliers : 1.37 % Allowed : 13.54 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6437 helix: 0.15 (0.10), residues: 2953 sheet: -1.65 (0.24), residues: 502 loop : -4.10 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP b 499 HIS 0.020 0.001 HIS i 482 PHE 0.016 0.001 PHE a 111 TYR 0.036 0.002 TYR l 486 ARG 0.006 0.000 ARG i 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 570 LYS cc_start: 0.3314 (mppt) cc_final: 0.2249 (mppt) REVERT: l 537 MET cc_start: 0.7659 (mmt) cc_final: 0.6663 (mmt) REVERT: k 77 MET cc_start: 0.8346 (mmp) cc_final: 0.8076 (mmp) REVERT: j 359 MET cc_start: 0.8090 (ptm) cc_final: 0.7726 (tmm) REVERT: j 528 MET cc_start: 0.8053 (mmp) cc_final: 0.7726 (mmm) REVERT: i 73 MET cc_start: 0.8365 (mmt) cc_final: 0.8083 (mmm) REVERT: i 338 MET cc_start: 0.5954 (ppp) cc_final: 0.5611 (ppp) REVERT: i 480 HIS cc_start: 0.8526 (m-70) cc_final: 0.8233 (m-70) REVERT: h 486 TYR cc_start: 0.5176 (t80) cc_final: 0.4513 (t80) REVERT: c 537 MET cc_start: 0.8507 (mtp) cc_final: 0.8258 (mtp) REVERT: d 42 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8318 (mm) REVERT: d 294 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7465 (t) REVERT: e 453 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.3624 (tmm) REVERT: e 466 MET cc_start: 0.8945 (pmm) cc_final: 0.8674 (pmm) REVERT: e 557 TYR cc_start: 0.5359 (m-80) cc_final: 0.4985 (m-80) REVERT: f 121 MET cc_start: 0.7986 (mmp) cc_final: 0.7193 (ptm) REVERT: f 437 GLN cc_start: -0.0425 (OUTLIER) cc_final: -0.1266 (tt0) outliers start: 64 outliers final: 29 residues processed: 367 average time/residue: 0.4570 time to fit residues: 289.5906 Evaluate side-chains 333 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 124 TRP Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 453 MET Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain c residue 577 THR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 294 VAL Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 437 GLN Chi-restraints excluded: chain f residue 447 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 517 optimal weight: 20.0000 chunk 352 optimal weight: 40.0000 chunk 9 optimal weight: 4.9990 chunk 462 optimal weight: 6.9990 chunk 256 optimal weight: 50.0000 chunk 530 optimal weight: 6.9990 chunk 429 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 317 optimal weight: 0.9980 chunk 557 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 ASN ** j 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 487 GLN f 108 ASN ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49719 Z= 0.201 Angle : 0.688 10.415 67383 Z= 0.359 Chirality : 0.043 0.187 7577 Planarity : 0.004 0.077 8946 Dihedral : 6.229 61.265 7017 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.80 % Favored : 80.91 % Rotamer: Outliers : 1.49 % Allowed : 15.33 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.10), residues: 6437 helix: 0.20 (0.10), residues: 2939 sheet: -1.73 (0.24), residues: 509 loop : -4.09 (0.10), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 499 HIS 0.022 0.001 HIS i 482 PHE 0.014 0.002 PHE a 111 TYR 0.035 0.002 TYR e 341 ARG 0.004 0.000 ARG h 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 303 time to evaluate : 4.338 Fit side-chains revert: symmetry clash REVERT: a 570 LYS cc_start: 0.3106 (mppt) cc_final: 0.2087 (mppt) REVERT: l 495 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6914 (pp) REVERT: j 359 MET cc_start: 0.8105 (ptm) cc_final: 0.7749 (tmm) REVERT: j 429 THR cc_start: 0.4134 (OUTLIER) cc_final: 0.3631 (m) REVERT: j 528 MET cc_start: 0.8095 (mmp) cc_final: 0.7860 (mmm) REVERT: i 73 MET cc_start: 0.8308 (mmt) cc_final: 0.8068 (mmm) REVERT: i 338 MET cc_start: 0.5918 (ppp) cc_final: 0.5587 (ppp) REVERT: h 486 TYR cc_start: 0.5174 (t80) cc_final: 0.4515 (t80) REVERT: c 112 MET cc_start: 0.8478 (mmm) cc_final: 0.8240 (mmp) REVERT: c 537 MET cc_start: 0.8502 (mtp) cc_final: 0.8244 (mtp) REVERT: d 294 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7483 (t) REVERT: e 453 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.3326 (tmm) REVERT: e 557 TYR cc_start: 0.5640 (m-80) cc_final: 0.5367 (m-80) REVERT: f 121 MET cc_start: 0.8025 (mmp) cc_final: 0.7200 (ptm) outliers start: 70 outliers final: 36 residues processed: 361 average time/residue: 0.4493 time to fit residues: 279.9969 Evaluate side-chains 334 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 77 MET Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 283 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 495 LEU Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 453 MET Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 294 VAL Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 447 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 209 optimal weight: 30.0000 chunk 559 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 364 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 622 optimal weight: 0.9980 chunk 516 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 18 HIS ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 450 ASN ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 593 GLN k 506 ASN ** j 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 ASN d 482 HIS d 503 ASN e 348 GLN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49719 Z= 0.184 Angle : 0.683 12.255 67383 Z= 0.354 Chirality : 0.043 0.376 7577 Planarity : 0.004 0.077 8946 Dihedral : 6.151 60.925 7017 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.63 % Favored : 81.08 % Rotamer: Outliers : 1.69 % Allowed : 15.97 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.10), residues: 6437 helix: 0.23 (0.10), residues: 2945 sheet: -1.73 (0.24), residues: 501 loop : -4.07 (0.10), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP b 499 HIS 0.020 0.001 HIS i 482 PHE 0.013 0.001 PHE a 467 TYR 0.042 0.001 TYR l 341 ARG 0.010 0.000 ARG b 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 314 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 22 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7763 (mm) REVERT: a 570 LYS cc_start: 0.2953 (mppt) cc_final: 0.2063 (mppt) REVERT: k 77 MET cc_start: 0.8345 (mmp) cc_final: 0.8052 (mmp) REVERT: j 359 MET cc_start: 0.8096 (ptm) cc_final: 0.7746 (tmm) REVERT: j 429 THR cc_start: 0.3925 (OUTLIER) cc_final: 0.3422 (m) REVERT: j 478 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (mp) REVERT: j 528 MET cc_start: 0.8179 (mmp) cc_final: 0.7873 (mmm) REVERT: h 486 TYR cc_start: 0.5181 (t80) cc_final: 0.4474 (t80) REVERT: c 112 MET cc_start: 0.8413 (mmm) cc_final: 0.8197 (mmp) REVERT: c 537 MET cc_start: 0.8491 (mtp) cc_final: 0.8232 (mtp) REVERT: d 294 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7554 (t) REVERT: e 453 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.3304 (tmm) REVERT: e 466 MET cc_start: 0.8660 (pmm) cc_final: 0.8242 (pmm) REVERT: e 557 TYR cc_start: 0.5832 (m-80) cc_final: 0.5479 (m-80) REVERT: f 121 MET cc_start: 0.8119 (mmp) cc_final: 0.7227 (ptm) outliers start: 79 outliers final: 47 residues processed: 379 average time/residue: 0.4629 time to fit residues: 298.3373 Evaluate side-chains 354 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 283 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 124 TRP Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 577 THR Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 541 VAL Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 453 MET Chi-restraints excluded: chain j residue 478 LEU Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain i residue 329 TYR Chi-restraints excluded: chain i residue 486 TYR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 133 THR Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 294 VAL Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 503 ASN Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 414 MET Chi-restraints excluded: chain f residue 447 MET Chi-restraints excluded: chain f residue 542 VAL Chi-restraints excluded: chain f residue 577 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 599 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 354 optimal weight: 0.0980 chunk 454 optimal weight: 7.9990 chunk 352 optimal weight: 50.0000 chunk 523 optimal weight: 30.0000 chunk 347 optimal weight: 50.0000 chunk 619 optimal weight: 0.0770 chunk 387 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 286 optimal weight: 6.9990 overall best weight: 5.0346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 ASN ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 221 HIS ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 482 HIS d 503 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 49719 Z= 0.200 Angle : 0.692 12.068 67383 Z= 0.358 Chirality : 0.043 0.230 7577 Planarity : 0.004 0.075 8946 Dihedral : 6.165 61.153 7017 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 18.95 % Favored : 80.77 % Rotamer: Outliers : 1.56 % Allowed : 16.91 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6437 helix: 0.25 (0.10), residues: 2946 sheet: -1.76 (0.24), residues: 509 loop : -4.07 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 499 HIS 0.021 0.001 HIS i 482 PHE 0.021 0.002 PHE l 118 TYR 0.032 0.002 TYR j 307 ARG 0.009 0.000 ARG b 474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 308 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 486 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6349 (t80) REVERT: a 476 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: a 537 MET cc_start: 0.8455 (mmm) cc_final: 0.8075 (mtp) REVERT: a 570 LYS cc_start: 0.2945 (OUTLIER) cc_final: 0.2072 (mppt) REVERT: k 77 MET cc_start: 0.8396 (mmp) cc_final: 0.8096 (mmp) REVERT: j 359 MET cc_start: 0.8016 (ptm) cc_final: 0.7729 (tmm) REVERT: j 429 THR cc_start: 0.3825 (OUTLIER) cc_final: 0.3332 (m) REVERT: j 478 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8264 (mp) REVERT: j 513 LEU cc_start: 0.6340 (mt) cc_final: 0.5984 (mt) REVERT: j 528 MET cc_start: 0.8165 (mmp) cc_final: 0.7892 (mmm) REVERT: h 355 MET cc_start: 0.0254 (mmp) cc_final: 0.0022 (mmp) REVERT: h 486 TYR cc_start: 0.5138 (t80) cc_final: 0.4370 (t80) REVERT: c 112 MET cc_start: 0.8482 (mmm) cc_final: 0.8276 (mmp) REVERT: c 537 MET cc_start: 0.8478 (mtp) cc_final: 0.8195 (mtp) REVERT: d 42 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (mm) REVERT: d 294 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7503 (t) REVERT: e 557 TYR cc_start: 0.5652 (m-80) cc_final: 0.5288 (m-80) REVERT: f 77 MET cc_start: 0.8084 (mmt) cc_final: 0.7611 (mmm) outliers start: 73 outliers final: 49 residues processed: 365 average time/residue: 0.4636 time to fit residues: 289.6350 Evaluate side-chains 356 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 283 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 486 TYR Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 476 PHE Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 570 LYS Chi-restraints excluded: chain a residue 577 THR Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 196 VAL Chi-restraints excluded: chain l residue 541 VAL Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 453 MET Chi-restraints excluded: chain j residue 478 LEU Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain i residue 329 TYR Chi-restraints excluded: chain i residue 486 TYR Chi-restraints excluded: chain i residue 532 MET Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 294 VAL Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 503 ASN Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 185 ILE Chi-restraints excluded: chain f residue 414 MET Chi-restraints excluded: chain f residue 447 MET Chi-restraints excluded: chain f residue 542 VAL Chi-restraints excluded: chain f residue 577 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 383 optimal weight: 7.9990 chunk 247 optimal weight: 30.0000 chunk 370 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 394 optimal weight: 9.9990 chunk 422 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 487 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 558 ASN ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 367 GLN k 506 ASN k 530 HIS ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 523 ASN ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 586 GLN d 126 GLN d 459 GLN d 482 HIS d 503 ASN e 450 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 GLN ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 49719 Z= 0.258 Angle : 0.736 12.468 67383 Z= 0.382 Chirality : 0.045 0.362 7577 Planarity : 0.005 0.074 8946 Dihedral : 6.379 61.420 7017 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.65 % Favored : 80.04 % Rotamer: Outliers : 1.73 % Allowed : 17.44 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.10), residues: 6437 helix: 0.09 (0.10), residues: 2961 sheet: -1.82 (0.24), residues: 511 loop : -4.14 (0.10), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 499 HIS 0.020 0.001 HIS i 482 PHE 0.027 0.002 PHE a 118 TYR 0.026 0.002 TYR e 341 ARG 0.008 0.001 ARG b 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 486 TYR cc_start: 0.6915 (OUTLIER) cc_final: 0.6478 (t80) REVERT: a 476 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: a 537 MET cc_start: 0.8401 (mmm) cc_final: 0.8027 (mtp) REVERT: l 44 TYR cc_start: 0.6894 (m-10) cc_final: 0.6376 (m-10) REVERT: k 42 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8269 (tp) REVERT: j 359 MET cc_start: 0.8041 (ptm) cc_final: 0.7767 (tmm) REVERT: j 429 THR cc_start: 0.3908 (OUTLIER) cc_final: 0.3388 (m) REVERT: j 513 LEU cc_start: 0.6330 (mt) cc_final: 0.5982 (mt) REVERT: j 528 MET cc_start: 0.8211 (mmp) cc_final: 0.7903 (mmm) REVERT: h 355 MET cc_start: 0.0681 (mmp) cc_final: 0.0477 (mmp) REVERT: h 486 TYR cc_start: 0.5154 (t80) cc_final: 0.4643 (t80) REVERT: c 537 MET cc_start: 0.8507 (mtp) cc_final: 0.8264 (mtp) REVERT: d 77 MET cc_start: 0.8289 (mmm) cc_final: 0.7732 (mmm) REVERT: d 431 ARG cc_start: 0.5503 (mtt180) cc_final: 0.4458 (ptt-90) REVERT: e 98 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: e 453 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3340 (tpp) REVERT: e 557 TYR cc_start: 0.5593 (m-80) cc_final: 0.5267 (m-80) REVERT: f 121 MET cc_start: 0.8106 (mmp) cc_final: 0.7333 (ptm) REVERT: f 329 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.6465 (m-10) outliers start: 81 outliers final: 53 residues processed: 374 average time/residue: 0.4624 time to fit residues: 296.8531 Evaluate side-chains 358 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 4.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 283 VAL Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 486 TYR Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 218 PHE Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 476 PHE Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 570 LYS Chi-restraints excluded: chain a residue 577 THR Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 196 VAL Chi-restraints excluded: chain l residue 541 VAL Chi-restraints excluded: chain k residue 42 LEU Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 194 ILE Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 333 HIS Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain i residue 120 VAL Chi-restraints excluded: chain i residue 290 THR Chi-restraints excluded: chain i residue 329 TYR Chi-restraints excluded: chain i residue 482 HIS Chi-restraints excluded: chain i residue 486 TYR Chi-restraints excluded: chain i residue 532 MET Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 503 ASN Chi-restraints excluded: chain e residue 98 GLU Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 329 TYR Chi-restraints excluded: chain f residue 542 VAL Chi-restraints excluded: chain f residue 577 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 563 optimal weight: 10.0000 chunk 593 optimal weight: 0.0870 chunk 541 optimal weight: 20.0000 chunk 577 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 251 optimal weight: 0.6980 chunk 453 optimal weight: 0.0370 chunk 177 optimal weight: 5.9990 chunk 521 optimal weight: 10.0000 chunk 546 optimal weight: 8.9990 chunk 575 optimal weight: 6.9990 overall best weight: 2.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 482 HIS ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 593 GLN k 506 ASN ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 503 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 49719 Z= 0.183 Angle : 0.705 12.128 67383 Z= 0.362 Chirality : 0.043 0.280 7577 Planarity : 0.004 0.077 8946 Dihedral : 6.169 60.949 7017 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.28 % Favored : 81.42 % Rotamer: Outliers : 1.45 % Allowed : 17.91 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.11), residues: 6437 helix: 0.20 (0.10), residues: 2974 sheet: -1.69 (0.24), residues: 504 loop : -4.10 (0.10), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP b 499 HIS 0.032 0.001 HIS a 482 PHE 0.022 0.001 PHE a 118 TYR 0.026 0.001 TYR k 44 ARG 0.007 0.000 ARG b 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 307 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 118 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.5286 (m-10) REVERT: b 486 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.6385 (t80) REVERT: a 476 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7516 (m-10) REVERT: a 537 MET cc_start: 0.8302 (mmm) cc_final: 0.7954 (mtp) REVERT: a 570 LYS cc_start: 0.3015 (OUTLIER) cc_final: 0.2473 (mppt) REVERT: l 224 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7632 (mmmt) REVERT: k 77 MET cc_start: 0.8427 (mmp) cc_final: 0.8129 (mmp) REVERT: k 112 MET cc_start: 0.7327 (mmp) cc_final: 0.7042 (mmm) REVERT: j 359 MET cc_start: 0.8094 (ptm) cc_final: 0.7812 (tmm) REVERT: j 429 THR cc_start: 0.3646 (OUTLIER) cc_final: 0.3175 (m) REVERT: j 513 LEU cc_start: 0.6311 (mt) cc_final: 0.5964 (mt) REVERT: j 528 MET cc_start: 0.8150 (mmp) cc_final: 0.7866 (mmm) REVERT: h 359 MET cc_start: 0.4824 (OUTLIER) cc_final: 0.3093 (ttm) REVERT: h 486 TYR cc_start: 0.5132 (t80) cc_final: 0.4663 (t80) REVERT: c 537 MET cc_start: 0.8487 (mtp) cc_final: 0.8204 (mtp) REVERT: d 42 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8428 (mm) REVERT: d 77 MET cc_start: 0.8173 (mmm) cc_final: 0.7556 (mmm) REVERT: d 431 ARG cc_start: 0.5400 (mtt180) cc_final: 0.4381 (ptt-90) REVERT: e 453 MET cc_start: 0.4045 (OUTLIER) cc_final: 0.3157 (ptt) REVERT: e 466 MET cc_start: 0.8600 (pmm) cc_final: 0.8175 (pmm) REVERT: e 557 TYR cc_start: 0.5761 (m-80) cc_final: 0.5461 (m-80) REVERT: f 77 MET cc_start: 0.8127 (mmt) cc_final: 0.7652 (mmm) REVERT: f 329 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.6127 (m-10) REVERT: f 447 MET cc_start: 0.1327 (OUTLIER) cc_final: 0.1073 (mtm) REVERT: f 535 TRP cc_start: -0.0747 (m100) cc_final: -0.0991 (m100) outliers start: 68 outliers final: 42 residues processed: 360 average time/residue: 0.4703 time to fit residues: 287.9205 Evaluate side-chains 350 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 118 PHE Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 486 TYR Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 476 PHE Chi-restraints excluded: chain a residue 570 LYS Chi-restraints excluded: chain a residue 577 THR Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 196 VAL Chi-restraints excluded: chain l residue 482 HIS Chi-restraints excluded: chain k residue 136 VAL Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 499 TRP Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain i residue 120 VAL Chi-restraints excluded: chain i residue 329 TYR Chi-restraints excluded: chain i residue 422 ARG Chi-restraints excluded: chain i residue 486 TYR Chi-restraints excluded: chain i residue 532 MET Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 503 ASN Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 329 TYR Chi-restraints excluded: chain f residue 414 MET Chi-restraints excluded: chain f residue 447 MET Chi-restraints excluded: chain f residue 542 VAL Chi-restraints excluded: chain f residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 379 optimal weight: 8.9990 chunk 610 optimal weight: 50.0000 chunk 372 optimal weight: 40.0000 chunk 289 optimal weight: 7.9990 chunk 424 optimal weight: 6.9990 chunk 640 optimal weight: 50.0000 chunk 589 optimal weight: 30.0000 chunk 510 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 394 optimal weight: 3.9990 chunk 312 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 444 GLN ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 ASN ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 503 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 49719 Z= 0.224 Angle : 0.729 12.584 67383 Z= 0.374 Chirality : 0.044 0.257 7577 Planarity : 0.004 0.075 8946 Dihedral : 6.285 61.160 7017 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.39 % Favored : 80.30 % Rotamer: Outliers : 1.37 % Allowed : 18.06 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6437 helix: 0.17 (0.10), residues: 2974 sheet: -1.78 (0.24), residues: 507 loop : -4.13 (0.10), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 499 HIS 0.023 0.001 HIS i 482 PHE 0.023 0.002 PHE a 118 TYR 0.041 0.002 TYR c 486 ARG 0.008 0.000 ARG b 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12874 Ramachandran restraints generated. 6437 Oldfield, 0 Emsley, 6437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 4.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 486 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.6415 (t80) REVERT: a 130 MET cc_start: 0.6425 (tpp) cc_final: 0.6168 (tpp) REVERT: a 476 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: a 537 MET cc_start: 0.8359 (mmm) cc_final: 0.7996 (mtp) REVERT: a 570 LYS cc_start: 0.2898 (OUTLIER) cc_final: 0.2256 (mppt) REVERT: l 537 MET cc_start: 0.7882 (mmm) cc_final: 0.7519 (mmm) REVERT: k 77 MET cc_start: 0.8459 (mmp) cc_final: 0.8150 (mmp) REVERT: j 359 MET cc_start: 0.8043 (ptm) cc_final: 0.7768 (tmm) REVERT: j 513 LEU cc_start: 0.6347 (mt) cc_final: 0.5997 (mt) REVERT: j 528 MET cc_start: 0.8193 (mmp) cc_final: 0.7879 (mmm) REVERT: h 359 MET cc_start: 0.4852 (OUTLIER) cc_final: 0.3314 (ttm) REVERT: h 486 TYR cc_start: 0.5084 (t80) cc_final: 0.4652 (t80) REVERT: c 537 MET cc_start: 0.8497 (mtp) cc_final: 0.8215 (mtp) REVERT: d 77 MET cc_start: 0.8352 (mmm) cc_final: 0.7818 (mmm) REVERT: d 431 ARG cc_start: 0.5456 (mtt180) cc_final: 0.4410 (ptt-90) REVERT: e 112 MET cc_start: 0.7278 (mmm) cc_final: 0.7060 (mmm) REVERT: e 453 MET cc_start: 0.4231 (OUTLIER) cc_final: 0.3633 (tpp) REVERT: e 466 MET cc_start: 0.8647 (pmm) cc_final: 0.8175 (pmm) REVERT: e 557 TYR cc_start: 0.5694 (m-80) cc_final: 0.5369 (m-80) REVERT: f 77 MET cc_start: 0.8069 (mmt) cc_final: 0.7589 (mmm) REVERT: f 112 MET cc_start: 0.7398 (mmp) cc_final: 0.7116 (mmp) REVERT: f 329 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6366 (m-10) REVERT: f 447 MET cc_start: 0.1397 (OUTLIER) cc_final: 0.1150 (mtm) outliers start: 64 outliers final: 49 residues processed: 350 average time/residue: 0.4643 time to fit residues: 277.9709 Evaluate side-chains 352 residues out of total 5690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 73 MET Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 197 LEU Chi-restraints excluded: chain b residue 308 VAL Chi-restraints excluded: chain b residue 486 TYR Chi-restraints excluded: chain b residue 492 VAL Chi-restraints excluded: chain b residue 549 VAL Chi-restraints excluded: chain b residue 551 VAL Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 476 PHE Chi-restraints excluded: chain a residue 482 HIS Chi-restraints excluded: chain a residue 570 LYS Chi-restraints excluded: chain a residue 577 THR Chi-restraints excluded: chain l residue 69 VAL Chi-restraints excluded: chain l residue 97 VAL Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 196 VAL Chi-restraints excluded: chain j residue 194 ILE Chi-restraints excluded: chain j residue 197 LEU Chi-restraints excluded: chain j residue 429 THR Chi-restraints excluded: chain j residue 482 HIS Chi-restraints excluded: chain j residue 492 VAL Chi-restraints excluded: chain j residue 517 VAL Chi-restraints excluded: chain i residue 120 VAL Chi-restraints excluded: chain i residue 329 TYR Chi-restraints excluded: chain i residue 422 ARG Chi-restraints excluded: chain i residue 486 TYR Chi-restraints excluded: chain i residue 532 MET Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 308 VAL Chi-restraints excluded: chain h residue 359 MET Chi-restraints excluded: chain h residue 414 MET Chi-restraints excluded: chain h residue 426 THR Chi-restraints excluded: chain h residue 502 VAL Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 308 VAL Chi-restraints excluded: chain c residue 341 TYR Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 133 THR Chi-restraints excluded: chain d residue 492 VAL Chi-restraints excluded: chain d residue 496 ARG Chi-restraints excluded: chain d residue 503 ASN Chi-restraints excluded: chain e residue 86 VAL Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 453 MET Chi-restraints excluded: chain e residue 517 VAL Chi-restraints excluded: chain e residue 519 ILE Chi-restraints excluded: chain f residue 138 VAL Chi-restraints excluded: chain f residue 329 TYR Chi-restraints excluded: chain f residue 414 MET Chi-restraints excluded: chain f residue 447 MET Chi-restraints excluded: chain f residue 542 VAL Chi-restraints excluded: chain f residue 577 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 405 optimal weight: 6.9990 chunk 543 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 141 optimal weight: 50.0000 chunk 510 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 524 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 ASN ** j 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 503 ASN ** e 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.075664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.048773 restraints weight = 372031.711| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 8.15 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49719 Z= 0.220 Angle : 0.732 12.353 67383 Z= 0.375 Chirality : 0.044 0.252 7577 Planarity : 0.004 0.098 8946 Dihedral : 6.287 60.619 7017 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.23 % Favored : 80.46 % Rotamer: Outliers : 1.45 % Allowed : 18.13 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.10), residues: 6437 helix: 0.16 (0.10), residues: 2974 sheet: -1.76 (0.24), residues: 505 loop : -4.14 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 499 HIS 0.022 0.001 HIS i 482 PHE 0.025 0.002 PHE a 118 TYR 0.037 0.002 TYR c 486 ARG 0.012 0.000 ARG a 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7288.85 seconds wall clock time: 130 minutes 14.83 seconds (7814.83 seconds total)