Starting phenix.real_space_refine on Mon Sep 30 09:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vus_43538/09_2024/8vus_43538.cif" } resolution = 3.99 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= 0.000 sd= 0.013 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 113 5.16 5 C 15979 2.51 5 N 4350 2.21 5 O 4564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25006 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1363 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "F" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1562 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1507 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 197} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1513 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 4964 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 31, 'TRANS': 630} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLU:plan': 27, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 203 Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 4630 Classifications: {'peptide': 654} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 26, 'TRANS': 627} Chain breaks: 1 Unresolved non-hydrogen bonds: 554 Unresolved non-hydrogen angles: 692 Unresolved non-hydrogen dihedrals: 437 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 23, 'PHE:plan': 2, 'GLU:plan': 33, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 359 Chain: "C" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4885 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 31, 'TRANS': 631} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 1, 'GLU:plan': 28, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 270 Chain: "D" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 4582 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 173} Link IDs: {'PTRANS': 25, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 693 Unresolved non-hydrogen dihedrals: 443 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 13, 'ASP:plan': 26, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 336 Time building chain proxies: 16.03, per 1000 atoms: 0.64 Number of scatterers: 25006 At special positions: 0 Unit cell: (113.848, 150.656, 197.736, 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 113 16.00 O 4564 8.00 N 4350 7.00 C 15979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 779 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 725 " - pdb=" SG CYS D 780 " 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: 6.14 Conformation dependent library (CDL) restraints added in 3.0 seconds 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6478 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 53 sheets defined 28.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 removed outlier: 4.078A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.657A pdb=" N GLN E 65 " --> pdb=" O PRO E 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 129 Processing helix chain 'F' and resid 185 through 190 removed outlier: 3.530A pdb=" N LYS F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 186 Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.586A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.623A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 103 through 114 removed outlier: 4.132A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.685A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.988A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.512A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLY A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 Processing helix chain 'A' and resid 316 through 327 removed outlier: 4.176A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 646 through 649 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 668 through 677 removed outlier: 4.067A pdb=" N ILE A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 694 through 704 removed outlier: 3.597A pdb=" N ALA A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 Processing helix chain 'A' and resid 749 through 764 Processing helix chain 'A' and resid 764 through 774 removed outlier: 3.586A pdb=" N ASP A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.175A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.913A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 232 through 245 removed outlier: 4.001A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.033A pdb=" N VAL B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 515 through 522 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.812A pdb=" N GLN B 651 " --> pdb=" O LYS B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 678 Processing helix chain 'B' and resid 678 through 686 removed outlier: 3.681A pdb=" N HIS B 682 " --> pdb=" O TYR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 702 Processing helix chain 'B' and resid 712 through 721 Processing helix chain 'B' and resid 751 through 765 Processing helix chain 'B' and resid 766 through 776 Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.755A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.560A pdb=" N SER C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.039A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 4.011A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.708A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.157A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.992A pdb=" N ILE C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 Processing helix chain 'C' and resid 317 through 327 removed outlier: 3.549A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.866A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.608A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 677 through 683 removed outlier: 3.785A pdb=" N MET C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 689 removed outlier: 4.149A pdb=" N MET C 687 " --> pdb=" O MET C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 704 Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 748 through 763 removed outlier: 4.614A pdb=" N ASN C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 774 removed outlier: 3.507A pdb=" N TRP C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 78 through 90 Processing helix chain 'D' and resid 107 through 119 removed outlier: 4.244A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 removed outlier: 3.630A pdb=" N ALA D 131 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.852A pdb=" N GLN D 216 " --> pdb=" O ASP D 212 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 222 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 4.041A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 311 removed outlier: 3.742A pdb=" N ARG D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 4.159A pdb=" N MET D 338 " --> pdb=" O HIS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.999A pdb=" N ASN D 447 " --> pdb=" O ASN D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.544A pdb=" N GLU D 520 " --> pdb=" O GLU D 516 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 removed outlier: 3.635A pdb=" N ARG D 672 " --> pdb=" O GLY D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 685 removed outlier: 4.090A pdb=" N TYR D 684 " --> pdb=" O TYR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 689 removed outlier: 4.237A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 712 through 721 Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 767 through 776 Processing sheet with id=AA1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.612A pdb=" N GLU E 10 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 112 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR E 109 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP E 36 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'E' and resid 122 through 126 removed outlier: 5.546A pdb=" N TYR E 173 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL E 178 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 122 through 126 removed outlier: 5.546A pdb=" N TYR E 173 " --> pdb=" O ASP E 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.773A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN F 89 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA9, first strand: chain 'F' and resid 116 through 120 removed outlier: 6.240A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 152 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.603A pdb=" N ALA H 92 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE H 50 " --> pdb=" O ARG H 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AB4, first strand: chain 'H' and resid 123 through 125 removed outlier: 3.714A pdb=" N ASP H 141 " --> pdb=" O TYR H 173 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N TYR H 173 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER H 174 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL H 166 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 148 through 151 removed outlier: 3.870A pdb=" N THR H 148 " --> pdb=" O ASN H 196 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TYR H 191 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS H 193 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS H 206 " --> pdb=" O CYS H 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.551A pdb=" N LEU L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 118 through 120 Processing sheet with id=AB9, first strand: chain 'L' and resid 147 through 152 Processing sheet with id=AC1, first strand: chain 'A' and resid 25 through 26 removed outlier: 5.441A pdb=" N LYS A 25 " --> pdb=" O ILE A 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.861A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.854A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.539A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 411 through 413 removed outlier: 3.597A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS A 436 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AC7, first strand: chain 'A' and resid 710 through 713 removed outlier: 3.887A pdb=" N VAL A 542 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 710 through 713 removed outlier: 6.703A pdb=" N GLN A 536 " --> pdb=" O ARG A 736 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ARG A 736 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.523A pdb=" N ILE B 36 " --> pdb=" O ASN B 68 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 38 through 39 removed outlier: 5.944A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AD3, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AD4, first strand: chain 'B' and resid 277 through 281 Processing sheet with id=AD5, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AD6, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.672A pdb=" N THR B 410 " --> pdb=" O TYR B 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 417 through 418 removed outlier: 3.775A pdb=" N VAL B 434 " --> pdb=" O CYS B 456 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 486 through 489 removed outlier: 3.831A pdb=" N LYS B 487 " --> pdb=" O ASN B 494 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 494 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 512 through 513 removed outlier: 4.395A pdb=" N LEU B 512 " --> pdb=" O GLY B 742 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AE2, first strand: chain 'B' and resid 533 through 536 Processing sheet with id=AE3, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.381A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 196 through 197 removed outlier: 8.324A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 221 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 267 through 271 removed outlier: 4.123A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 365 through 366 Processing sheet with id=AE7, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.843A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.670A pdb=" N CYS C 436 " --> pdb=" O GLN C 453 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 455 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AF1, first strand: chain 'C' and resid 517 through 518 removed outlier: 4.512A pdb=" N LEU C 517 " --> pdb=" O GLY C 740 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 536 " --> pdb=" O SER C 737 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 38 through 40 Processing sheet with id=AF3, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AF4, first strand: chain 'D' and resid 278 through 281 Processing sheet with id=AF5, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AF6, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.969A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AF8, first strand: chain 'D' and resid 708 through 711 825 hydrogen bonds defined for protein. 2256 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: 9.34 Time building geometry restraints manager: 7.12 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: 8156 1.34 - 1.46: 6188 1.46 - 1.58: 11067 1.58 - 1.70: 0 1.70 - 1.82: 175 Bond restraints: 25586 Sorted by residual: bond pdb=" C ILE A 380 " pdb=" N TRP A 381 " ideal model delta sigma weight residual 1.333 1.251 0.082 2.74e-02 1.33e+03 8.85e+00 bond pdb=" CB LYS D 270 " pdb=" CG LYS D 270 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB TRP A 56 " pdb=" CG TRP A 56 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.92e+00 bond pdb=" CB PRO A 413 " pdb=" CG PRO A 413 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.88e+00 bond pdb=" C ASN F 93 " pdb=" N TRP F 94 " ideal model delta sigma weight residual 1.331 1.309 0.022 1.59e-02 3.96e+03 1.86e+00 ... (remaining 25581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 34601 2.68 - 5.37: 310 5.37 - 8.05: 38 8.05 - 10.74: 6 10.74 - 13.42: 2 Bond angle restraints: 34957 Sorted by residual: angle pdb=" C ASN F 93 " pdb=" N TRP F 94 " pdb=" CA TRP F 94 " ideal model delta sigma weight residual 122.38 108.96 13.42 2.90e+00 1.19e-01 2.14e+01 angle pdb=" C ASP D 655 " pdb=" CA ASP D 655 " pdb=" CB ASP D 655 " ideal model delta sigma weight residual 116.34 110.58 5.76 1.40e+00 5.10e-01 1.70e+01 angle pdb=" CA CYS A 79 " pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CB MET D 338 " pdb=" CG MET D 338 " pdb=" SD MET D 338 " ideal model delta sigma weight residual 112.70 123.19 -10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CA MET D 338 " pdb=" CB MET D 338 " pdb=" CG MET D 338 " ideal model delta sigma weight residual 114.10 120.99 -6.89 2.00e+00 2.50e-01 1.19e+01 ... (remaining 34952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 12958 17.69 - 35.37: 1639 35.37 - 53.06: 383 53.06 - 70.75: 57 70.75 - 88.44: 31 Dihedral angle restraints: 15068 sinusoidal: 5013 harmonic: 10055 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual 93.00 168.11 -75.11 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CA VAL H 101 " pdb=" C VAL H 101 " pdb=" N PHE H 102 " pdb=" CA PHE H 102 " ideal model delta harmonic sigma weight residual -180.00 -139.05 -40.95 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 15065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3219 0.052 - 0.104: 706 0.104 - 0.156: 133 0.156 - 0.208: 6 0.208 - 0.260: 3 Chirality restraints: 4067 Sorted by residual: chirality pdb=" CG LEU C 296 " pdb=" CB LEU C 296 " pdb=" CD1 LEU C 296 " pdb=" CD2 LEU C 296 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE A 400 " pdb=" CA ILE A 400 " pdb=" CG1 ILE A 400 " pdb=" CG2 ILE A 400 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA THR C 105 " pdb=" N THR C 105 " pdb=" C THR C 105 " pdb=" CB THR C 105 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4064 not shown) Planarity restraints: 4483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.054 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO A 413 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 181 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO H 182 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 182 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 182 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 319 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " 0.035 5.00e-02 4.00e+02 ... (remaining 4480 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 496 2.66 - 3.22: 24203 3.22 - 3.78: 36781 3.78 - 4.34: 44996 4.34 - 4.90: 74998 Nonbonded interactions: 181474 Sorted by model distance: nonbonded pdb=" O SER E 99 " pdb=" OG SER E 99 " model vdw 2.100 3.040 nonbonded pdb=" OE1 GLU A 39 " pdb=" OG SER A 64 " model vdw 2.109 3.040 nonbonded pdb=" OD1 ASP C 671 " pdb=" OH TYR C 684 " model vdw 2.132 3.040 nonbonded pdb=" OG SER D 171 " pdb=" O ASN D 202 " model vdw 2.162 3.040 nonbonded pdb=" O PHE B 660 " pdb=" OH TYR B 684 " model vdw 2.171 3.040 ... (remaining 181469 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 23 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 53 or resid 55 through 82 or (resi \ d 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throug \ h 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or re \ sid 95 through 98 or (resid 99 through 100 and (name N or name CA or name C or n \ ame O or name CB )) or resid 101 through 152 or (resid 153 and (name N or name C \ A or name C or name O or name CB )) or resid 154 through 155 or (resid 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 168 or \ (resid 169 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 191 or (resid 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 216 or (resid 217 and (name N or name CA or \ name C or name O or name CB )) or resid 218 through 226 or (resid 227 through 2 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 230 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 through 271 or (resid 272 and (name N or name CA or name C or name O or \ name CB )) or resid 273 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 282 or (resid 283 through 284 a \ nd (name N or name CA or name C or name O or name CB )) or resid 285 through 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 through 308 or (resid 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 326 or (resid 327 and (name N or name CA or name C \ or name O or name CB )) or resid 328 through 342 or (resid 343 and (name N or na \ me CA or name C or name O or name CB )) or resid 344 through 353 or (resid 354 a \ nd (name N or name CA or name C or name O or name CB )) or resid 355 through 357 \ or resid 359 through 375 or (resid 376 and (name N or name CA or name C or name \ O or name CB )) or resid 377 through 384 or (resid 385 and (name N or name CA o \ r name C or name O or name CB )) or resid 386 through 415 or (resid 416 through \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 or (re \ sid 419 and (name N or name CA or name C or name O or name CB )) or resid 420 or \ (resid 421 through 424 and (name N or name CA or name C or name O or name CB )) \ or resid 425 through 426 or (resid 427 and (name N or name CA or name C or name \ O or name CB )) or resid 428 or (resid 429 and (name N or name CA or name C or \ name O or name CB )) or resid 430 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 450 or (resid 451 and \ (name N or name CA or name C or name O or name CB )) or resid 452 through 469 or \ (resid 470 and (name N or name CA or name C or name O or name CB )) or resid 47 \ 1 through 488 or (resid 489 and (name N or name CA or name C or name O or name C \ B )) or resid 490 or (resid 491 through 492 and (name N or name CA or name C or \ name O or name CB )) or resid 493 through 497 or (resid 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 510 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 542 or \ (resid 543 through 546 and (name N or name CA or name C or name O or name CB )) \ or resid 641 through 642 or (resid 643 and (name N or name CA or name C or name \ O or name CB )) or resid 644 or (resid 645 and (name N or name CA or name C or \ name O or name CB )) or resid 646 through 650 or (resid 651 and (name N or name \ CA or name C or name O or name CB )) or resid 652 or (resid 653 through 655 and \ (name N or name CA or name C or name O or name CB )) or resid 656 or (resid 657 \ through 659 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 0 through 663 or (resid 664 through 667 and (name N or name CA or name C or name \ O or name CB )) or resid 668 through 675 or (resid 676 and (name N or name CA o \ r name C or name O or name CB )) or resid 677 through 679 or (resid 680 and (nam \ e N or name CA or name C or name O or name CB )) or resid 681 through 684 or (re \ sid 685 and (name N or name CA or name C or name O or name CB )) or resid 686 or \ (resid 687 through 688 and (name N or name CA or name C or name O or name CB )) \ or resid 689 through 692 or (resid 693 and (name N or name CA or name C or name \ O or name CB )) or resid 694 through 696 or (resid 697 through 698 and (name N \ or name CA or name C or name O or name CB )) or resid 699 through 703 or (resid \ 704 and (name N or name CA or name C or name O or name CB )) or resid 705 throug \ h 723 or (resid 724 and (name N or name CA or name C or name O or name CB )) or \ resid 725 through 731 or (resid 732 and (name N or name CA or name C or name O o \ r name CB )) or resid 733 through 744 or (resid 745 through 746 and (name N or n \ ame CA or name C or name O or name CB )) or resid 747 through 750 or (resid 751 \ and (name N or name CA or name C or name O or name CB )) or resid 752 through 76 \ 1 or (resid 762 and (name N or name CA or name C or name O or name CB )) or resi \ d 763 through 769 or (resid 770 through 771 and (name N or name CA or name C or \ name O or name CB )) or resid 772 through 775 or (resid 776 through 778 and (nam \ e N or name CA or name C or name O or name CB )) or resid 779)) selection = (chain 'C' and (resid 23 through 53 or resid 55 through 57 or (resid 58 and (nam \ e N or name CA or name C or name O or name CB )) or resid 59 through 72 or (resi \ d 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 through 171 or (resid 172 and (name N or name CA or name C or name O or n \ ame CB )) or resid 173 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 through 184 or (resid 185 through 186 and \ (name N or name CA or name C or name O or name CB )) or resid 187 or (resid 188 \ and (name N or name CA or name C or name O or name CB )) or resid 189 through 2 \ 01 or (resid 202 and (name N or name CA or name C or name O or name CB )) or res \ id 203 through 207 or (resid 208 through 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 218 or (resid 219 and (name N or \ name CA or name C or name O or name CB )) or resid 220 through 237 or (resid 238 \ and (name N or name CA or name C or name O or name CB )) or resid 239 through 2 \ 54 or (resid 255 and (name N or name CA or name C or name O or name CB )) or res \ id 256 or (resid 257 through 258 and (name N or name CA or name C or name O or n \ ame CB )) or resid 259 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 296 or (resid 297 through 300 and \ (name N or name CA or name C or name O or name CB )) or resid 301 through 302 o \ r (resid 303 through 304 and (name N or name CA or name C or name O or name CB ) \ ) or resid 305 through 310 or (resid 311 and (name N or name CA or name C or nam \ e O or name CB )) or resid 312 through 322 or (resid 323 and (name N or name CA \ or name C or name O or name CB )) or resid 324 through 328 or (resid 329 and (na \ me N or name CA or name C or name O or name CB )) or resid 330 through 336 or (r \ esid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 t \ hrough 357 or resid 359 through 377 or (resid 378 and (name N or name CA or name \ C or name O or name CB )) or resid 379 through 389 or (resid 390 and (name N or \ name CA or name C or name O or name CB )) or resid 391 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 395 or (resi \ d 396 and (name N or name CA or name C or name O or name CB )) or resid 397 thro \ ugh 411 or (resid 412 and (name N or name CA or name C or name O or name CB )) o \ r resid 413 through 447 or (resid 448 through 449 and (name N or name CA or name \ C or name O or name CB )) or resid 450 through 474 or (resid 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 482 or (resid 48 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 484 through \ 485 or (resid 486 and (name N or name CA or name C or name O or name CB )) or re \ sid 487 through 493 or resid 495 through 501 or (resid 502 and (name N or name C \ A or name C or name O or name CB )) or resid 503 through 677 or (resid 678 throu \ gh 680 and (name N or name CA or name C or name O or name CB )) or resid 681 thr \ ough 690 or (resid 691 and (name N or name CA or name C or name O or name CB )) \ or resid 692 through 726 or (resid 727 and (name N or name CA or name C or name \ O or name CB )) or resid 728 through 766 or (resid 767 and (name N or name CA or \ name C or name O or name CB )) or resid 768 through 774 or (resid 775 through 7 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 779)) } ncs_group { reference = (chain 'B' and (resid 35 through 41 or (resid 42 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 76 or (resid 77 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 through \ 89 or (resid 90 through 91 and (name N or name CA or name C or name O or name C \ B )) or (resid 92 through 96 and (name N or name CA or name C or name O or name \ CB )) or resid 97 through 101 or (resid 102 through 108 and (name N or name CA o \ r name C or name O or name CB )) or resid 109 through 113 or (resid 114 and (nam \ e N or name CA or name C or name O or name CB )) or resid 115 through 127 or (re \ sid 128 and (name N or name CA or name C or name O or name CB )) or resid 129 th \ rough 149 or (resid 150 and (name N or name CA or name C or name O or name CB )) \ or resid 151 through 180 or (resid 181 through 182 and (name N or name CA or na \ me C or name O or name CB )) or resid 183 through 201 or (resid 202 and (name N \ or name CA or name C or name O or name CB )) or resid 203 through 208 or (resid \ 209 through 211 and (name N or name CA or name C or name O or name CB )) or resi \ d 212 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB )) or resid 221 through 231 or (resid 232 and (name N or name CA or name C \ or name O or name CB )) or resid 233 through 259 or (resid 260 and (name N or n \ ame CA or name C or name O or name CB )) or resid 261 through 281 or (resid 282 \ through 283 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 4 or (resid 285 and (name N or name CA or name C or name O or name CB )) or resi \ d 286 or (resid 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 303 or (resid 304 through 306 and (name N or name CA or name C \ or name O or name CB )) or resid 307 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 330 or (resid 331 \ through 333 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 4 through 343 or (resid 344 and (name N or name CA or name C or name O or name C \ B )) or resid 345 or (resid 346 and (name N or name CA or name C or name O or na \ me CB )) or resid 347 through 365 or (resid 366 and (name N or name CA or name C \ or name O or name CB )) or resid 367 through 381 or (resid 382 and (name N or n \ ame CA or name C or name O or name CB )) or resid 383 or (resid 384 and (name N \ or name CA or name C or name O or name CB )) or resid 385 through 394 or (resid \ 395 and (name N or name CA or name C or name O or name CB )) or resid 396 or (re \ sid 397 through 398 and (name N or name CA or name C or name O or name CB )) or \ resid 404 through 422 or (resid 423 and (name N or name CA or name C or name O o \ r name CB )) or resid 424 through 437 or (resid 438 and (name N or name CA or na \ me C or name O or name CB )) or resid 439 or (resid 440 through 448 and (name N \ or name CA or name C or name O or name CB )) or resid 449 through 471 or (resid \ 472 and (name N or name CA or name C or name O or name CB )) or resid 473 or (re \ sid 474 and (name N or name CA or name C or name O or name CB )) or resid 475 th \ rough 480 or (resid 481 through 482 and (name N or name CA or name C or name O o \ r name CB )) or resid 483 or (resid 484 and (name N or name CA or name C or name \ O or name CB )) or resid 485 through 493 or (resid 494 and (name N or name CA o \ r name C or name O or name CB )) or resid 495 through 510 or (resid 511 and (nam \ e N or name CA or name C or name O or name CB )) or resid 512 through 522 or (re \ sid 523 and (name N or name CA or name C or name O or name CB )) or resid 524 or \ (resid 525 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 6 through 535 or (resid 536 and (name N or name CA or name C or name O or name C \ B )) or resid 537 or (resid 538 and (name N or name CA or name C or name O or na \ me CB )) or resid 539 through 540 or (resid 541 through 643 and (name N or name \ CA or name C or name O or name CB )) or resid 644 through 646 or (resid 647 and \ (name N or name CA or name C or name O or name CB )) or resid 648 through 663 or \ (resid 664 through 665 and (name N or name CA or name C or name O or name CB )) \ or resid 666 through 669 or (resid 670 and (name N or name CA or name C or name \ O or name CB )) or resid 671 through 676 or (resid 677 and (name N or name CA o \ r name C or name O or name CB )) or resid 678 through 682 or (resid 683 and (nam \ e N or name CA or name C or name O or name CB )) or resid 684 through 685 or (re \ sid 686 through 687 and (name N or name CA or name C or name O or name CB )) or \ resid 688 or (resid 689 and (name N or name CA or name C or name O or name CB )) \ or resid 690 through 696 or (resid 697 through 698 and (name N or name CA or na \ me C or name O or name CB )) or resid 699 through 700 or (resid 701 through 702 \ and (name N or name CA or name C or name O or name CB )) or (resid 703 through 7 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 708 through \ 720 or (resid 721 through 723 and (name N or name CA or name C or name O or nam \ e CB )) or resid 724 through 733 or (resid 734 through 737 and (name N or name C \ A or name C or name O or name CB )) or resid 738 through 766 or (resid 767 and ( \ name N or name CA or name C or name O or name CB )) or resid 768 through 780 or \ (resid 781 through 784 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'D' and (resid 35 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or (resid 41 through 54 and (name N or name CA or name \ C or name O or name CB )) or resid 55 through 66 or (resid 67 through 72 and (n \ ame N or name CA or name C or name O or name CB )) or resid 73 or (resid 74 and \ (name N or name CA or name C or name O or name CB )) or resid 75 or (resid 76 th \ rough 78 and (name N or name CA or name C or name O or name CB )) or resid 79 th \ rough 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) \ or resid 138 through 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 181 or (resid 182 and (name N or name CA o \ r name C or name O or name CB )) or resid 183 through 198 or (resid 199 through \ 200 and (name N or name CA or name C or name O or name CB )) or resid 201 throug \ h 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or \ resid 208 through 209 or (resid 210 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 217 or (resid 218 and (name N or n \ ame CA or name C or name O or name CB )) or resid 219 through 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 24 \ 1 or (resid 242 through 243 and (name N or name CA or name C or name O or name C \ B )) or resid 244 through 265 or (resid 266 and (name N or name CA or name C or \ name O or name CB )) or resid 267 or (resid 268 and (name N or name CA or name C \ or name O or name CB )) or resid 269 or (resid 270 through 271 and (name N or n \ ame CA or name C or name O or name CB )) or resid 272 through 311 or (resid 312 \ and (name N or name CA or name C or name O or name CB )) or resid 313 through 32 \ 5 or (resid 326 and (name N or name CA or name C or name O or name CB )) or resi \ d 327 through 355 or (resid 356 and (name N or name CA or name C or name O or na \ me CB )) or resid 357 through 367 or (resid 368 through 369 and (name N or name \ CA or name C or name O or name CB )) or resid 370 through 391 or (resid 392 and \ (name N or name CA or name C or name O or name CB )) or resid 393 through 405 or \ (resid 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 or (resid 408 and (name N or name CA or name C or name O or name CB )) or resi \ d 409 through 410 or (resid 411 through 414 and (name N or name CA or name C or \ name O or name CB )) or resid 415 or (resid 416 and (name N or name CA or name C \ or name O or name CB )) or resid 417 through 418 or (resid 419 through 421 and \ (name N or name CA or name C or name O or name CB )) or resid 422 through 431 or \ (resid 432 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 3 through 519 or (resid 520 and (name N or name CA or name C or name O or name C \ B )) or resid 521 through 641 or (resid 642 through 643 and (name N or name CA o \ r name C or name O or name CB )) or resid 644 through 655 or (resid 656 through \ 657 and (name N or name CA or name C or name O or name CB )) or resid 658 throug \ h 694 or (resid 695 through 698 and (name N or name CA or name C or name O or na \ me CB )) or resid 699 through 746 or (resid 747 and (name N or name CA or name C \ or name O or name CB )) or resid 748 through 752 or (resid 753 and (name N or n \ ame CA or name C or name O or name CB )) or resid 754 through 768 or (resid 769 \ through 770 and (name N or name CA or name C or name O or name CB )) or resid 77 \ 1 through 773 or (resid 774 and (name N or name CA or name C or name O or name C \ B )) or resid 775 through 778 or (resid 779 and (name N or name CA or name C or \ name O or name CB )) or resid 780 through 784)) } ncs_group { reference = (chain 'E' and (resid 1 through 89 or (resid 90 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 113 or (resid 114 throug \ h 116 and (name N or name CA or name C or name O or name CB )) or resid 117 thro \ ugh 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) o \ r resid 140 through 211)) selection = (chain 'H' and (resid 1 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 81 or (resid 82 and (name N or name \ CA or name C or name O or name CB )) or resid 83 through 114 or (resid 115 thro \ ugh 116 and (name N or name CA or name C or name O or name CB )) or resid 117 or \ (resid 118 through 119 and (name N or name CA or name C or name O or name CB )) \ or resid 120 or (resid 121 through 128 and (name N or name CA or name C or name \ O or name CB )) or resid 129 through 130 or resid 135 through 141 or (resid 142 \ and (name N or name CA or name C or name O or name CB )) or resid 143 through 1 \ 46 or (resid 147 through 153 and (name N or name CA or name C or name O or name \ CB )) or (resid 154 through 157 and (name N or name CA or name C or name O or na \ me CB )) or resid 158 through 167 or (resid 168 through 170 and (name N or name \ CA or name C or name O or name CB )) or (resid 171 through 180 and (name N or na \ me CA or name C or name O or name CB )) or resid 181 through 182 or (resid 183 t \ hrough 186 and (name N or name CA or name C or name O or name CB )) or resid 187 \ or (resid 188 through 191 and (name N or name CA or name C or name O or name CB \ )) or resid 192 or (resid 193 through 200 and (name N or name CA or name C or n \ ame O or name CB )) or resid 201 through 211)) } ncs_group { reference = (chain 'F' and (resid 1 through 69 or (resid 70 through 71 and (name N or name C \ A or name C or name O or name CB )) or resid 72 through 123 or (resid 124 throug \ h 129 and (name N or name CA or name C or name O or name CB )) or resid 130 or ( \ resid 131 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 144 or (resid 145 through 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 or (resid 151 through 158 and (name N or \ name CA or name C or name O or name CB )) or resid 159 or (resid 160 and (name \ N or name CA or name C or name O or name CB )) or resid 161 or (resid 162 and (n \ ame N or name CA or name C or name O or name CB )) or resid 163 through 181 or ( \ resid 182 and (name N or name CA or name C or name O or name CB )) or resid 183 \ through 188 or (resid 189 through 192 and (name N or name CA or name C or name O \ or name CB )) or resid 193 through 209 or (resid 210 through 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 1 through 9 or (resid 10 through 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 36 or (resid 37 and (name \ N or name CA or name C or name O or name CB )) or resid 38 through 41 or (resid \ 42 through 43 and (name N or name CA or name C or name O or name CB )) or resid \ 44 through 53 or (resid 54 through 55 and (name N or name CA or name C or name \ O or name CB )) or resid 56 through 70 or (resid 71 and (name N or name CA or na \ me C or name O or name CB )) or resid 72 through 74 or (resid 75 through 78 and \ (name N or name CA or name C or name O or name CB )) or resid 79 through 82 or ( \ resid 83 through 85 and (name N or name CA or name C or name O or name CB )) or \ resid 86 through 101 or (resid 102 and (name N or name CA or name C or name O or \ name CB )) or resid 103 through 189 or (resid 190 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 215)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.460 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: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 58.900 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.004 0.082 25586 Z= 0.262 Angle : 0.668 13.424 34957 Z= 0.349 Chirality : 0.044 0.260 4067 Planarity : 0.005 0.080 4483 Dihedral : 16.760 88.436 8521 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.21 % Favored : 86.36 % Rotamer: Outliers : 0.34 % Allowed : 37.38 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.35 (0.15), residues: 3445 helix: 1.11 (0.19), residues: 835 sheet: -2.18 (0.18), residues: 798 loop : -2.65 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 33 HIS 0.012 0.001 HIS F 200 PHE 0.014 0.001 PHE C 710 TYR 0.017 0.001 TYR H 95 ARG 0.003 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 3.022 Fit side-chains revert: symmetry clash REVERT: B 450 MET cc_start: 0.8949 (tpt) cc_final: 0.8046 (pmm) REVERT: C 502 MET cc_start: 0.8861 (mmt) cc_final: 0.8497 (mmp) outliers start: 8 outliers final: 1 residues processed: 135 average time/residue: 0.2983 time to fit residues: 70.8893 Evaluate side-chains 123 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 10.0000 chunk 260 optimal weight: 0.0870 chunk 144 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 269 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 163 optimal weight: 0.0270 chunk 200 optimal weight: 0.4980 chunk 312 optimal weight: 9.9990 overall best weight: 2.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN A 67 HIS A 761 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25586 Z= 0.271 Angle : 0.641 11.746 34957 Z= 0.337 Chirality : 0.045 0.217 4067 Planarity : 0.005 0.068 4483 Dihedral : 4.923 40.083 3692 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.15 % Favored : 86.42 % Rotamer: Outliers : 4.40 % Allowed : 34.60 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.28 (0.15), residues: 3445 helix: 1.21 (0.18), residues: 859 sheet: -2.12 (0.19), residues: 785 loop : -2.70 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 33 HIS 0.008 0.001 HIS F 200 PHE 0.014 0.001 PHE C 710 TYR 0.022 0.001 TYR F 49 ARG 0.007 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 131 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 145 GLU cc_start: 0.8447 (pm20) cc_final: 0.8230 (mp0) REVERT: L 1 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8322 (pp20) REVERT: L 167 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: A 164 ILE cc_start: 0.9308 (pt) cc_final: 0.9032 (mp) REVERT: A 201 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7979 (p) REVERT: A 761 HIS cc_start: 0.6432 (OUTLIER) cc_final: 0.5913 (t-90) REVERT: B 450 MET cc_start: 0.9000 (tpt) cc_final: 0.8111 (pmm) REVERT: C 296 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8711 (mp) REVERT: C 502 MET cc_start: 0.8929 (mmt) cc_final: 0.8524 (mmp) REVERT: C 523 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7870 (mtt180) REVERT: D 74 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6831 (tmm) outliers start: 103 outliers final: 51 residues processed: 227 average time/residue: 0.3217 time to fit residues: 124.1963 Evaluate side-chains 180 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 122 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 736 ARG Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 312 optimal weight: 8.9990 chunk 338 optimal weight: 0.4980 chunk 278 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS B 154 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25586 Z= 0.198 Angle : 0.600 11.031 34957 Z= 0.313 Chirality : 0.044 0.197 4067 Planarity : 0.004 0.067 4483 Dihedral : 4.741 40.309 3690 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.61 % Favored : 87.95 % Rotamer: Outliers : 5.25 % Allowed : 32.59 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.15 (0.15), residues: 3445 helix: 1.36 (0.18), residues: 858 sheet: -2.03 (0.19), residues: 788 loop : -2.64 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 33 HIS 0.006 0.001 HIS F 200 PHE 0.012 0.001 PHE D 147 TYR 0.014 0.001 TYR F 49 ARG 0.004 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 139 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 23 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8886 (ptpp) REVERT: L 1 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8330 (pp20) REVERT: L 167 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: A 164 ILE cc_start: 0.9277 (pt) cc_final: 0.8966 (mp) REVERT: A 201 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 385 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: A 761 HIS cc_start: 0.6582 (OUTLIER) cc_final: 0.5902 (t-90) REVERT: B 181 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8547 (tpp80) REVERT: B 450 MET cc_start: 0.9002 (tpt) cc_final: 0.8134 (pmm) REVERT: C 158 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6081 (t80) REVERT: C 296 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8671 (mp) REVERT: C 502 MET cc_start: 0.8886 (mmt) cc_final: 0.8603 (mmp) REVERT: C 523 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7964 (mtt180) REVERT: C 767 GLU cc_start: 0.8650 (tp30) cc_final: 0.8406 (tp30) REVERT: D 74 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6832 (tmm) REVERT: D 89 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7478 (tt) REVERT: D 204 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 256 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5878 (mt) outliers start: 123 outliers final: 72 residues processed: 252 average time/residue: 0.3123 time to fit residues: 132.9134 Evaluate side-chains 214 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 128 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 371 HIS Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 736 ARG Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 314 optimal weight: 20.0000 chunk 332 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 499 ASN C 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 25586 Z= 0.635 Angle : 0.819 13.668 34957 Z= 0.438 Chirality : 0.050 0.231 4067 Planarity : 0.006 0.070 4483 Dihedral : 5.602 38.304 3690 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 16.46 % Favored : 83.08 % Rotamer: Outliers : 8.59 % Allowed : 31.35 % Favored : 60.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.63 (0.14), residues: 3445 helix: 0.84 (0.18), residues: 854 sheet: -2.47 (0.18), residues: 832 loop : -2.78 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP E 33 HIS 0.012 0.002 HIS C 53 PHE 0.023 0.002 PHE C 42 TYR 0.028 0.002 TYR F 49 ARG 0.009 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 125 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8382 (pp20) REVERT: L 167 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 164 ILE cc_start: 0.9408 (pt) cc_final: 0.9165 (mp) REVERT: A 201 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7976 (p) REVERT: A 354 MET cc_start: 0.6824 (mpp) cc_final: 0.6503 (mpp) REVERT: A 736 ARG cc_start: 0.5123 (OUTLIER) cc_final: 0.4362 (mmm-85) REVERT: A 761 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5602 (t-90) REVERT: B 90 MET cc_start: 0.8449 (tmm) cc_final: 0.8163 (tmm) REVERT: C 158 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6666 (t80) REVERT: C 177 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8876 (pp30) REVERT: C 296 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9071 (mp) REVERT: C 499 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.9185 (p0) REVERT: C 502 MET cc_start: 0.9022 (mmt) cc_final: 0.8771 (mmp) REVERT: C 523 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7971 (mtt180) REVERT: C 720 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8339 (mm-30) REVERT: C 768 ASP cc_start: 0.8433 (m-30) cc_final: 0.8140 (p0) REVERT: D 74 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6640 (tmm) REVERT: D 89 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7560 (tt) REVERT: D 204 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7871 (mp) REVERT: D 205 THR cc_start: 0.7889 (m) cc_final: 0.7671 (m) REVERT: D 216 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7800 (mm110) REVERT: D 227 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8325 (tp) REVERT: D 334 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8442 (tt) REVERT: D 348 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7683 (pp) outliers start: 201 outliers final: 124 residues processed: 316 average time/residue: 0.3227 time to fit residues: 169.1368 Evaluate side-chains 263 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 121 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 453 LYS Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 650 PHE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 499 ASN Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 720 GLU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 507 MET Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 247 optimal weight: 0.7980 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS B 96 HIS B 746 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25586 Z= 0.227 Angle : 0.637 12.234 34957 Z= 0.331 Chirality : 0.045 0.216 4067 Planarity : 0.005 0.068 4483 Dihedral : 5.088 40.258 3690 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.25 % Favored : 87.29 % Rotamer: Outliers : 5.64 % Allowed : 33.79 % Favored : 60.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.32 (0.15), residues: 3445 helix: 1.27 (0.18), residues: 851 sheet: -2.24 (0.18), residues: 793 loop : -2.71 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 33 HIS 0.010 0.001 HIS C 101 PHE 0.018 0.001 PHE A 102 TYR 0.016 0.001 TYR B 281 ARG 0.003 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 130 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8403 (pp20) REVERT: L 167 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 83 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8936 (mm) REVERT: A 201 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7889 (p) REVERT: A 354 MET cc_start: 0.6732 (mpp) cc_final: 0.6371 (mpp) REVERT: A 535 TYR cc_start: 0.7198 (m-80) cc_final: 0.6816 (m-80) REVERT: A 761 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5724 (t-90) REVERT: B 90 MET cc_start: 0.8363 (tmm) cc_final: 0.8119 (tmm) REVERT: B 125 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9211 (pp) REVERT: B 147 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6771 (t80) REVERT: B 450 MET cc_start: 0.9010 (tpt) cc_final: 0.7948 (pmm) REVERT: C 158 TYR cc_start: 0.6653 (OUTLIER) cc_final: 0.6175 (t80) REVERT: C 177 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8817 (pp30) REVERT: C 296 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8856 (mp) REVERT: C 363 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: C 502 MET cc_start: 0.8955 (mmt) cc_final: 0.8692 (mmp) REVERT: C 523 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8074 (mtt180) REVERT: C 735 PHE cc_start: 0.7976 (t80) cc_final: 0.7748 (t80) REVERT: C 767 GLU cc_start: 0.8698 (tp30) cc_final: 0.8436 (tp30) REVERT: D 74 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6648 (tmm) REVERT: D 89 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7449 (tt) REVERT: D 256 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5974 (mt) REVERT: D 334 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (tp) outliers start: 132 outliers final: 87 residues processed: 252 average time/residue: 0.3079 time to fit residues: 131.3480 Evaluate side-chains 227 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 124 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 650 PHE Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 8.9990 chunk 299 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 82 optimal weight: 0.0570 chunk 332 optimal weight: 9.9990 chunk 276 optimal weight: 0.0770 chunk 154 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 overall best weight: 3.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25586 Z= 0.326 Angle : 0.658 12.102 34957 Z= 0.344 Chirality : 0.045 0.217 4067 Planarity : 0.005 0.067 4483 Dihedral : 5.102 39.693 3690 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.34 % Favored : 85.20 % Rotamer: Outliers : 6.88 % Allowed : 33.49 % Favored : 59.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.36 (0.15), residues: 3445 helix: 1.25 (0.18), residues: 851 sheet: -2.30 (0.18), residues: 804 loop : -2.71 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 33 HIS 0.009 0.001 HIS C 101 PHE 0.030 0.001 PHE A 674 TYR 0.019 0.002 TYR F 49 ARG 0.004 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 127 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: L 167 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: A 164 ILE cc_start: 0.9350 (pt) cc_final: 0.9099 (mp) REVERT: A 201 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 275 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7557 (mttm) REVERT: A 535 TYR cc_start: 0.7213 (m-80) cc_final: 0.6740 (m-80) REVERT: A 761 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5857 (t-90) REVERT: B 90 MET cc_start: 0.8365 (tmm) cc_final: 0.8124 (tmm) REVERT: B 125 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9172 (pp) REVERT: B 147 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6876 (t80) REVERT: B 450 MET cc_start: 0.8987 (tpt) cc_final: 0.7932 (pmm) REVERT: B 671 GLU cc_start: 0.8350 (pm20) cc_final: 0.7986 (pm20) REVERT: C 158 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.6357 (t80) REVERT: C 296 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8886 (mp) REVERT: C 363 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 502 MET cc_start: 0.9023 (mmt) cc_final: 0.8695 (mmp) REVERT: C 523 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8054 (mtt180) REVERT: C 767 GLU cc_start: 0.8780 (tp30) cc_final: 0.8528 (tp30) REVERT: C 768 ASP cc_start: 0.8388 (m-30) cc_final: 0.8060 (p0) REVERT: C 774 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8110 (m) REVERT: D 74 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6687 (tmm) REVERT: D 89 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7501 (tt) REVERT: D 204 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7826 (mp) REVERT: D 205 THR cc_start: 0.7966 (m) cc_final: 0.7719 (m) REVERT: D 256 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5939 (mt) REVERT: D 334 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 161 outliers final: 115 residues processed: 278 average time/residue: 0.3008 time to fit residues: 142.7055 Evaluate side-chains 256 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 124 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 650 PHE Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 736 ARG Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 390 TRP Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 185 optimal weight: 0.0570 chunk 331 optimal weight: 50.0000 chunk 207 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 overall best weight: 2.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25586 Z= 0.305 Angle : 0.655 12.002 34957 Z= 0.340 Chirality : 0.045 0.215 4067 Planarity : 0.005 0.066 4483 Dihedral : 5.082 39.808 3690 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.56 % Favored : 86.01 % Rotamer: Outliers : 7.09 % Allowed : 33.66 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.30 (0.15), residues: 3445 helix: 1.30 (0.18), residues: 852 sheet: -2.22 (0.18), residues: 800 loop : -2.71 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 33 HIS 0.009 0.001 HIS C 101 PHE 0.034 0.001 PHE A 674 TYR 0.017 0.001 TYR F 49 ARG 0.003 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 131 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8387 (pp20) REVERT: L 167 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: A 79 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6369 (t) REVERT: A 164 ILE cc_start: 0.9345 (pt) cc_final: 0.9094 (mp) REVERT: A 201 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 275 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7525 (mttm) REVERT: A 354 MET cc_start: 0.6724 (mpp) cc_final: 0.6426 (mpp) REVERT: A 535 TYR cc_start: 0.7262 (m-80) cc_final: 0.6663 (m-80) REVERT: A 761 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5900 (t-90) REVERT: B 90 MET cc_start: 0.8353 (tmm) cc_final: 0.8114 (tmm) REVERT: B 125 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9267 (pp) REVERT: B 147 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 450 MET cc_start: 0.8993 (tpt) cc_final: 0.7956 (pmm) REVERT: C 158 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6388 (t80) REVERT: C 296 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8853 (mp) REVERT: C 363 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8102 (tm-30) REVERT: C 502 MET cc_start: 0.8993 (mmt) cc_final: 0.8693 (mmp) REVERT: C 523 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8039 (mtt180) REVERT: C 720 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: C 767 GLU cc_start: 0.8736 (tp30) cc_final: 0.8472 (tp30) REVERT: C 774 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8097 (m) REVERT: D 74 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6694 (tmm) REVERT: D 89 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7493 (tt) REVERT: D 205 THR cc_start: 0.8016 (m) cc_final: 0.7810 (m) REVERT: D 256 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6050 (mt) REVERT: D 334 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (tt) outliers start: 166 outliers final: 126 residues processed: 288 average time/residue: 0.3128 time to fit residues: 154.0216 Evaluate side-chains 271 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 127 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 650 PHE Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 720 GLU Chi-restraints excluded: chain C residue 736 ARG Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 773 TRP Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 390 TRP Chi-restraints excluded: chain D residue 497 ILE Chi-restraints excluded: chain D residue 517 GLU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 163 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25586 Z= 0.189 Angle : 0.618 11.198 34957 Z= 0.315 Chirality : 0.044 0.210 4067 Planarity : 0.004 0.066 4483 Dihedral : 4.799 40.530 3690 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.34 % Favored : 87.29 % Rotamer: Outliers : 5.94 % Allowed : 34.64 % Favored : 59.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.11 (0.15), residues: 3445 helix: 1.47 (0.18), residues: 854 sheet: -2.07 (0.19), residues: 789 loop : -2.62 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 33 HIS 0.009 0.001 HIS C 101 PHE 0.029 0.001 PHE A 674 TYR 0.015 0.001 TYR B 180 ARG 0.003 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 132 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8384 (pp20) REVERT: L 167 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: A 164 ILE cc_start: 0.9314 (pt) cc_final: 0.9050 (mp) REVERT: A 201 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 275 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7519 (mttm) REVERT: A 354 MET cc_start: 0.6647 (mpp) cc_final: 0.6337 (mpp) REVERT: A 535 TYR cc_start: 0.7165 (m-80) cc_final: 0.6782 (m-80) REVERT: A 761 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5909 (t-90) REVERT: B 82 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8354 (tt) REVERT: B 90 MET cc_start: 0.8350 (tmm) cc_final: 0.8124 (tmm) REVERT: B 125 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9236 (pp) REVERT: B 147 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6876 (t80) REVERT: B 281 TYR cc_start: 0.8077 (t80) cc_final: 0.7566 (t80) REVERT: B 450 MET cc_start: 0.8973 (tpt) cc_final: 0.7982 (pmm) REVERT: C 158 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6052 (t80) REVERT: C 296 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 363 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: C 502 MET cc_start: 0.8979 (mmt) cc_final: 0.8645 (mmp) REVERT: C 523 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8040 (mtt180) REVERT: C 768 ASP cc_start: 0.8345 (m-30) cc_final: 0.8004 (p0) REVERT: C 774 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8076 (m) REVERT: D 74 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6683 (tmm) REVERT: D 89 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7446 (tt) REVERT: D 256 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6084 (mt) REVERT: D 334 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8531 (tt) REVERT: D 413 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.4365 (mt-10) outliers start: 139 outliers final: 104 residues processed: 263 average time/residue: 0.3073 time to fit residues: 137.1929 Evaluate side-chains 247 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 125 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 736 ARG Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 774 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 390 TRP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 9.9990 chunk 317 optimal weight: 0.0770 chunk 289 optimal weight: 10.0000 chunk 308 optimal weight: 0.4980 chunk 185 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 242 optimal weight: 0.0170 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 0.4980 chunk 292 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 32 ASN A 761 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 25586 Z= 0.161 Angle : 0.615 10.847 34957 Z= 0.310 Chirality : 0.043 0.205 4067 Planarity : 0.004 0.066 4483 Dihedral : 4.589 40.663 3690 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.35 % Favored : 88.27 % Rotamer: Outliers : 4.53 % Allowed : 36.22 % Favored : 59.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.97 (0.15), residues: 3445 helix: 1.60 (0.18), residues: 859 sheet: -1.89 (0.19), residues: 778 loop : -2.60 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 33 HIS 0.012 0.001 HIS A 761 PHE 0.027 0.001 PHE A 674 TYR 0.014 0.001 TYR H 95 ARG 0.003 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 138 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8393 (pp20) REVERT: L 167 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 164 ILE cc_start: 0.9270 (pt) cc_final: 0.8846 (mm) REVERT: A 201 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7912 (p) REVERT: A 354 MET cc_start: 0.6594 (mpp) cc_final: 0.6274 (mpp) REVERT: A 535 TYR cc_start: 0.7138 (m-80) cc_final: 0.6890 (m-80) REVERT: A 761 HIS cc_start: 0.6229 (OUTLIER) cc_final: 0.5833 (t-90) REVERT: B 90 MET cc_start: 0.8368 (tmm) cc_final: 0.8124 (tmm) REVERT: B 125 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9198 (pp) REVERT: B 147 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 281 TYR cc_start: 0.7974 (t80) cc_final: 0.7456 (t80) REVERT: B 450 MET cc_start: 0.8958 (tpt) cc_final: 0.7996 (pmm) REVERT: C 158 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.6027 (t80) REVERT: C 296 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8730 (mp) REVERT: C 502 MET cc_start: 0.8923 (mmt) cc_final: 0.8636 (mmp) REVERT: C 523 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7982 (mtt180) REVERT: C 767 GLU cc_start: 0.8682 (tp30) cc_final: 0.8433 (tp30) REVERT: C 768 ASP cc_start: 0.8357 (m-30) cc_final: 0.7968 (p0) REVERT: D 74 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6641 (tmm) REVERT: D 89 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 216 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: D 256 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5911 (mt) outliers start: 106 outliers final: 78 residues processed: 237 average time/residue: 0.2991 time to fit residues: 122.2169 Evaluate side-chains 226 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 135 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 773 TRP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 753 ARG Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 30.0000 chunk 326 optimal weight: 0.9990 chunk 199 optimal weight: 0.0770 chunk 154 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 342 optimal weight: 40.0000 chunk 315 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 25586 Z= 0.274 Angle : 0.668 15.214 34957 Z= 0.338 Chirality : 0.044 0.209 4067 Planarity : 0.005 0.066 4483 Dihedral : 4.757 39.019 3690 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.89 % Favored : 86.73 % Rotamer: Outliers : 4.78 % Allowed : 36.14 % Favored : 59.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.02 (0.15), residues: 3445 helix: 1.56 (0.18), residues: 863 sheet: -1.99 (0.19), residues: 788 loop : -2.60 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 33 HIS 0.016 0.001 HIS F 200 PHE 0.022 0.001 PHE A 674 TYR 0.016 0.001 TYR F 49 ARG 0.003 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6890 Ramachandran restraints generated. 3445 Oldfield, 0 Emsley, 3445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 137 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: L 167 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 164 ILE cc_start: 0.9313 (pt) cc_final: 0.9028 (mp) REVERT: A 201 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (p) REVERT: A 275 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7570 (mttm) REVERT: A 354 MET cc_start: 0.6664 (mpp) cc_final: 0.6353 (mpp) REVERT: A 535 TYR cc_start: 0.7143 (m-80) cc_final: 0.6833 (m-80) REVERT: A 761 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5959 (t-90) REVERT: B 90 MET cc_start: 0.8339 (tmm) cc_final: 0.8110 (tmm) REVERT: B 125 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9140 (pp) REVERT: B 450 MET cc_start: 0.8989 (tpt) cc_final: 0.8005 (pmm) REVERT: C 158 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.6202 (t80) REVERT: C 296 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8829 (mp) REVERT: C 502 MET cc_start: 0.8955 (mmt) cc_final: 0.8667 (mmp) REVERT: C 523 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8007 (mtt180) REVERT: C 768 ASP cc_start: 0.8337 (m-30) cc_final: 0.8054 (p0) REVERT: D 74 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6557 (tmm) REVERT: D 89 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7514 (tt) REVERT: D 256 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5941 (mt) REVERT: D 413 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.3935 (mt-10) outliers start: 112 outliers final: 92 residues processed: 242 average time/residue: 0.2910 time to fit residues: 122.5039 Evaluate side-chains 238 residues out of total 3036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 133 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain L residue 1 GLU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 SER Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 167 GLU Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 56 TRP Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 761 HIS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 746 GLN Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 773 TRP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 660 PHE Chi-restraints excluded: chain D residue 710 TYR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 762 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 251 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 273 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 HIS ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.111684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081652 restraints weight = 88188.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075967 restraints weight = 78296.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076282 restraints weight = 83518.372| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.005 0.062 25586 Z= 0.353 Angle : 0.701 13.495 34957 Z= 0.359 Chirality : 0.046 0.304 4067 Planarity : 0.005 0.067 4483 Dihedral : 4.999 39.112 3690 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.96 % Favored : 85.60 % Rotamer: Outliers : 5.55 % Allowed : 35.92 % Favored : 58.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.15 (0.15), residues: 3445 helix: 1.39 (0.18), residues: 868 sheet: -2.10 (0.19), residues: 787 loop : -2.64 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 33 HIS 0.015 0.001 HIS F 200 PHE 0.027 0.001 PHE A 674 TYR 0.022 0.002 TYR B 281 ARG 0.004 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.55 seconds wall clock time: 79 minutes 38.43 seconds (4778.43 seconds total)