Starting phenix.real_space_refine on Sun Feb 18 13:56:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h93_34552/02_2024/8h93_34552.pdb" } resolution = 3.01 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= 0.046 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 181 5.16 5 C 14111 2.51 5 N 3795 2.21 5 O 4104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 544": "OD1" <-> "OD2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 790": "OD1" <-> "OD2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 409": "OD1" <-> "OD2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D ASP 544": "OD1" <-> "OD2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D GLU 567": "OE1" <-> "OE2" Residue "D GLU 627": "OE1" <-> "OE2" Residue "D PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 646": "OD1" <-> "OD2" Residue "D ASP 853": "OD1" <-> "OD2" Residue "D TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E ASP 507": "OD1" <-> "OD2" Residue "E PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7481 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "D" Number of atoms: 7476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7476 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 26, 'TRANS': 922} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2898 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 719 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Time building chain proxies: 11.66, per 1000 atoms: 0.53 Number of scatterers: 22191 At special positions: 0 Unit cell: (101.2, 101.2, 226.6, 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 181 16.00 O 4104 8.00 N 3795 7.00 C 14111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 4.6 seconds 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5344 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 41.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.508A pdb=" N VAL A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.759A pdb=" N SER A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 292 through 304 Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.874A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'A' and resid 329 through 346 removed outlier: 3.614A pdb=" N LYS A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 373 Processing helix chain 'A' and resid 380 through 401 Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.746A pdb=" N LEU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 444 through 462 removed outlier: 3.660A pdb=" N VAL A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY A 460 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.892A pdb=" N GLY A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 518 through 532 removed outlier: 3.730A pdb=" N LYS A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 removed outlier: 4.025A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 562 removed outlier: 3.502A pdb=" N VAL A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.917A pdb=" N LYS A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 639 removed outlier: 3.709A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 684 through 695 removed outlier: 3.748A pdb=" N PHE A 693 " --> pdb=" O TRP A 689 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 738 through 751 Processing helix chain 'A' and resid 766 through 779 removed outlier: 3.531A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'A' and resid 852 through 865 removed outlier: 3.818A pdb=" N ASN A 865 " --> pdb=" O MET A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 893 removed outlier: 3.615A pdb=" N GLU A 893 " --> pdb=" O GLU A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 923 Processing helix chain 'A' and resid 937 through 950 removed outlier: 3.912A pdb=" N GLN A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 978 removed outlier: 4.433A pdb=" N ALA A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1007 Processing helix chain 'A' and resid 1018 through 1022 Processing helix chain 'A' and resid 1023 through 1037 Processing helix chain 'A' and resid 1045 through 1049 removed outlier: 3.581A pdb=" N ALA A1048 " --> pdb=" O ASP A1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.533A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.853A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER C 42 " --> pdb=" O ILE C 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 37 through 42' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.859A pdb=" N GLY C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 Processing helix chain 'C' and resid 94 through 114 removed outlier: 3.531A pdb=" N GLU C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.691A pdb=" N LYS D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.618A pdb=" N ALA D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 198 removed outlier: 4.063A pdb=" N GLU D 197 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 211 removed outlier: 3.789A pdb=" N THR D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 210 " --> pdb=" O THR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 removed outlier: 4.097A pdb=" N SER D 227 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 255 removed outlier: 3.628A pdb=" N LEU D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 280 removed outlier: 4.426A pdb=" N LEU D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.521A pdb=" N ASN D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.718A pdb=" N ASN D 320 " --> pdb=" O SER D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.040A pdb=" N PHE D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP D 325 " --> pdb=" O HIS D 321 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 346 Processing helix chain 'D' and resid 356 through 373 removed outlier: 3.603A pdb=" N LYS D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 444 through 459 removed outlier: 4.170A pdb=" N TYR D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 462 No H-bonds generated for 'chain 'D' and resid 460 through 462' Processing helix chain 'D' and resid 488 through 498 Processing helix chain 'D' and resid 500 through 512 removed outlier: 3.692A pdb=" N LEU D 510 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 511 " --> pdb=" O LEU D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 532 removed outlier: 3.613A pdb=" N LYS D 522 " --> pdb=" O THR D 518 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL D 527 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 552 removed outlier: 3.572A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 574 through 586 removed outlier: 4.185A pdb=" N LYS D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 639 Processing helix chain 'D' and resid 653 through 665 removed outlier: 3.576A pdb=" N LEU D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 695 removed outlier: 3.736A pdb=" N LEU D 688 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 693 " --> pdb=" O TRP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 722 removed outlier: 3.627A pdb=" N MET D 713 " --> pdb=" O LYS D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 751 removed outlier: 3.913A pdb=" N MET D 744 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 745 " --> pdb=" O GLY D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 779 Processing helix chain 'D' and resid 795 through 807 removed outlier: 3.589A pdb=" N LEU D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 802 " --> pdb=" O SER D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 836 removed outlier: 3.562A pdb=" N VAL D 827 " --> pdb=" O GLY D 823 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 836 " --> pdb=" O GLN D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 865 removed outlier: 3.929A pdb=" N GLY D 857 " --> pdb=" O ASP D 853 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 865 " --> pdb=" O MET D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 892 Processing helix chain 'D' and resid 910 through 923 removed outlier: 4.192A pdb=" N GLU D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 921 " --> pdb=" O ALA D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 951 removed outlier: 3.736A pdb=" N GLY D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 947 " --> pdb=" O THR D 943 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 951 " --> pdb=" O GLY D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 979 removed outlier: 3.543A pdb=" N CYS D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1006 Processing helix chain 'D' and resid 1018 through 1022 removed outlier: 3.699A pdb=" N TYR D1022 " --> pdb=" O LYS D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1037 removed outlier: 3.520A pdb=" N GLU D1034 " --> pdb=" O LEU D1030 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 removed outlier: 3.566A pdb=" N LEU E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 163 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG E 174 " --> pdb=" O PHE E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.697A pdb=" N VAL F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER F 42 " --> pdb=" O ILE F 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 37 through 42' Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.716A pdb=" N ARG F 56 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 73 Processing helix chain 'F' and resid 94 through 114 removed outlier: 3.563A pdb=" N ARG F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 178 removed outlier: 6.755A pdb=" N ILE A 175 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP A 220 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE A 177 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 217 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR A 267 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 219 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ARG A 269 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 145 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS A 144 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR A 285 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 432 removed outlier: 4.124A pdb=" N CYS A 439 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 571 removed outlier: 3.503A pdb=" N ILE A 594 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 675 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 674 " --> pdb=" O ASN A 702 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY A 704 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 731 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 759 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 732 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 761 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 790 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 847 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 873 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 875 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 961 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 989 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.519A pdb=" N ASP B 328 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 289 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 576 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 289 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 574 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 296 through 300 removed outlier: 4.360A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 346 through 351 removed outlier: 3.526A pdb=" N ALA B 360 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 369 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 396 removed outlier: 3.598A pdb=" N TRP B 414 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 404 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 412 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 423 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP B 415 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 421 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 434 through 438 removed outlier: 3.872A pdb=" N GLY B 445 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU B 451 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 464 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS B 453 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 455 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 460 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 471 through 475 removed outlier: 6.524A pdb=" N GLY B 486 " --> pdb=" O MET B 472 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU B 474 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 484 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS B 492 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 513 through 518 removed outlier: 3.521A pdb=" N LYS B 517 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 529 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE B 534 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN B 547 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 536 " --> pdb=" O LEU B 545 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 50 removed outlier: 3.836A pdb=" N GLU C 88 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 79 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.709A pdb=" N PHE D 177 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 145 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR D 285 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 567 through 571 Processing sheet with id=AB6, first strand: chain 'D' and resid 644 through 645 removed outlier: 3.657A pdb=" N LEU D 674 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 702 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 761 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 788 " --> pdb=" O LEU D 758 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS D 816 " --> pdb=" O LEU D 787 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 873 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 872 " --> pdb=" O GLU D 900 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU D 901 " --> pdb=" O ASP D 930 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 961 " --> pdb=" O LEU D 931 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL D 989 " --> pdb=" O LEU D 960 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 327 through 328 removed outlier: 8.623A pdb=" N ASP E 328 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL E 289 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU E 284 " --> pdb=" O LYS E 580 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS E 580 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS E 286 " --> pdb=" O HIS E 578 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS E 578 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 288 " --> pdb=" O VAL E 576 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 307 through 312 removed outlier: 3.651A pdb=" N VAL E 318 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER E 333 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 346 through 351 removed outlier: 3.845A pdb=" N THR E 348 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 358 " --> pdb=" O TRP E 371 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 370 " --> pdb=" O LYS E 381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 395 through 396 removed outlier: 3.545A pdb=" N ALA E 404 " --> pdb=" O ARG E 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 412 " --> pdb=" O ALA E 404 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL E 411 " --> pdb=" O ASN E 424 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN E 424 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE E 413 " --> pdb=" O VAL E 422 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 420 " --> pdb=" O ASP E 415 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 436 through 437 removed outlier: 3.868A pdb=" N ARG E 452 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 451 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 464 " --> pdb=" O LEU E 451 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS E 453 " --> pdb=" O SER E 462 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP E 455 " --> pdb=" O LYS E 460 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS E 460 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 471 through 476 removed outlier: 6.284A pdb=" N GLY E 486 " --> pdb=" O MET E 472 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 474 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 484 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N HIS E 476 " --> pdb=" O TRP E 482 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N TRP E 482 " --> pdb=" O HIS E 476 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS E 493 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN E 491 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASP E 507 " --> pdb=" O HIS E 492 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU E 494 " --> pdb=" O THR E 505 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR E 505 " --> pdb=" O LEU E 494 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 515 through 518 removed outlier: 3.755A pdb=" N LYS E 517 " --> pdb=" O ALA E 526 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 534 " --> pdb=" O GLN E 547 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN E 547 " --> pdb=" O ILE E 534 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL E 536 " --> pdb=" O LEU E 545 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 47 through 50 removed outlier: 3.963A pdb=" N GLU F 88 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2688 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: 8.90 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5118 1.33 - 1.45: 4619 1.45 - 1.58: 12629 1.58 - 1.70: 0 1.70 - 1.83: 255 Bond restraints: 22621 Sorted by residual: bond pdb=" N VAL B 150 " pdb=" CA VAL B 150 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N VAL C 46 " pdb=" CA VAL C 46 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.45e+00 bond pdb=" N VAL F 46 " pdb=" CA VAL F 46 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.05e+00 bond pdb=" N ILE F 38 " pdb=" CA ILE F 38 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.67e+00 bond pdb=" N VAL C 41 " pdb=" CA VAL C 41 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 22616 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.55: 382 105.55 - 112.75: 12425 112.75 - 119.95: 7547 119.95 - 127.15: 10008 127.15 - 134.35: 277 Bond angle restraints: 30639 Sorted by residual: angle pdb=" N PRO F 44 " pdb=" CA PRO F 44 " pdb=" C PRO F 44 " ideal model delta sigma weight residual 113.40 124.41 -11.01 1.34e+00 5.57e-01 6.76e+01 angle pdb=" C PRO C 44 " pdb=" CA PRO C 44 " pdb=" CB PRO C 44 " ideal model delta sigma weight residual 111.23 103.08 8.15 1.28e+00 6.10e-01 4.05e+01 angle pdb=" C ALA D 561 " pdb=" N LEU D 562 " pdb=" CA LEU D 562 " ideal model delta sigma weight residual 123.05 115.82 7.23 1.40e+00 5.10e-01 2.67e+01 angle pdb=" C PRO F 44 " pdb=" CA PRO F 44 " pdb=" CB PRO F 44 " ideal model delta sigma weight residual 112.55 105.58 6.97 1.50e+00 4.44e-01 2.16e+01 angle pdb=" CA SER F 42 " pdb=" C SER F 42 " pdb=" O SER F 42 " ideal model delta sigma weight residual 120.55 116.06 4.49 1.06e+00 8.90e-01 1.79e+01 ... (remaining 30634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11928 17.97 - 35.94: 1363 35.94 - 53.91: 306 53.91 - 71.88: 57 71.88 - 89.84: 39 Dihedral angle restraints: 13693 sinusoidal: 5495 harmonic: 8198 Sorted by residual: dihedral pdb=" CD ARG C 32 " pdb=" NE ARG C 32 " pdb=" CZ ARG C 32 " pdb=" NH1 ARG C 32 " ideal model delta sinusoidal sigma weight residual 0.00 -73.21 73.21 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CD ARG D 564 " pdb=" NE ARG D 564 " pdb=" CZ ARG D 564 " pdb=" NH1 ARG D 564 " ideal model delta sinusoidal sigma weight residual 0.00 47.97 -47.97 1 1.00e+01 1.00e-02 3.17e+01 dihedral pdb=" CA LYS D 170 " pdb=" C LYS D 170 " pdb=" N MET D 171 " pdb=" CA MET D 171 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 13690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2899 0.052 - 0.104: 485 0.104 - 0.156: 122 0.156 - 0.208: 18 0.208 - 0.260: 4 Chirality restraints: 3528 Sorted by residual: chirality pdb=" CA ILE A 771 " pdb=" N ILE A 771 " pdb=" C ILE A 771 " pdb=" CB ILE A 771 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA LEU C 45 " pdb=" N LEU C 45 " pdb=" C LEU C 45 " pdb=" CB LEU C 45 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO F 44 " pdb=" N PRO F 44 " pdb=" C PRO F 44 " pdb=" CB PRO F 44 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3525 not shown) Planarity restraints: 3878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 32 " -1.054 9.50e-02 1.11e+02 4.72e-01 1.35e+02 pdb=" NE ARG C 32 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 32 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 32 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 32 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 564 " -0.815 9.50e-02 1.11e+02 3.65e-01 8.11e+01 pdb=" NE ARG D 564 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG D 564 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 564 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 564 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 452 " 0.672 9.50e-02 1.11e+02 3.01e-01 5.54e+01 pdb=" NE ARG B 452 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG B 452 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 452 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 452 " 0.021 2.00e-02 2.50e+03 ... (remaining 3875 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 488 2.69 - 3.25: 22354 3.25 - 3.80: 34553 3.80 - 4.35: 44642 4.35 - 4.90: 72405 Nonbonded interactions: 174442 Sorted by model distance: nonbonded pdb=" OE2 GLU B 550 " pdb=" OH TYR B 577 " model vdw 2.143 2.440 nonbonded pdb=" OG1 THR D 966 " pdb=" OD1 ASN D 968 " model vdw 2.195 2.440 nonbonded pdb=" O LYS D 690 " pdb=" OG SER D 694 " model vdw 2.201 2.440 nonbonded pdb=" O ALA A 864 " pdb=" OG1 THR A 895 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR D 856 " pdb=" O PRO D 878 " model vdw 2.214 2.440 ... (remaining 174437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 97 through 723 or (resid 724 through 725 and (name N or na \ me CA or name C or name O or name CB )) or resid 726 through 1059)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 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: 14.590 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 62.640 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 86.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22621 Z= 0.217 Angle : 0.679 11.015 30639 Z= 0.400 Chirality : 0.044 0.260 3528 Planarity : 0.012 0.472 3878 Dihedral : 16.454 89.845 8349 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.08 % Allowed : 14.73 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.19 (0.16), residues: 2790 helix: 1.82 (0.16), residues: 1029 sheet: -0.09 (0.22), residues: 578 loop : -1.32 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 629 HIS 0.008 0.001 HIS A 104 PHE 0.025 0.001 PHE D 177 TYR 0.014 0.001 TYR D1023 ARG 0.006 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TRP cc_start: 0.7183 (p90) cc_final: 0.6896 (p90) REVERT: A 225 MET cc_start: 0.5194 (mmt) cc_final: 0.4690 (mmp) REVERT: A 279 MET cc_start: 0.5437 (pmm) cc_final: 0.4880 (mtm) REVERT: A 699 LYS cc_start: 0.7447 (mppt) cc_final: 0.6865 (mppt) REVERT: A 754 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6893 (mpt180) REVERT: A 854 ASP cc_start: 0.7006 (t70) cc_final: 0.6627 (t0) REVERT: A 964 LYS cc_start: 0.7513 (tmmt) cc_final: 0.7185 (tmmt) REVERT: B 359 PHE cc_start: 0.7285 (m-80) cc_final: 0.7025 (m-10) REVERT: B 451 LEU cc_start: 0.6753 (mp) cc_final: 0.6303 (mp) REVERT: B 458 MET cc_start: 0.5754 (ppp) cc_final: 0.5512 (mmt) REVERT: B 474 LEU cc_start: 0.8337 (mm) cc_final: 0.8062 (mp) REVERT: D 122 MET cc_start: 0.4659 (tpt) cc_final: 0.4285 (mmt) REVERT: D 137 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6345 (tm-30) REVERT: D 366 PHE cc_start: 0.5931 (m-10) cc_final: 0.5698 (m-80) REVERT: D 401 MET cc_start: 0.4337 (mtt) cc_final: 0.4096 (mtm) REVERT: D 487 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7106 (ptp-170) REVERT: D 565 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: D 622 LYS cc_start: 0.5693 (tppt) cc_final: 0.5205 (tttt) REVERT: D 657 MET cc_start: 0.7341 (tpt) cc_final: 0.6900 (tpt) REVERT: D 668 SER cc_start: 0.7795 (t) cc_final: 0.7457 (t) REVERT: D 744 MET cc_start: 0.7652 (mpp) cc_final: 0.7266 (mtm) REVERT: D 854 ASP cc_start: 0.7400 (p0) cc_final: 0.6888 (t0) REVERT: D 919 MET cc_start: 0.6217 (tmm) cc_final: 0.5656 (tmm) REVERT: D 1021 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5614 (mt-10) REVERT: E 401 MET cc_start: 0.4286 (pmm) cc_final: 0.3971 (pmm) REVERT: E 439 ASP cc_start: 0.7556 (p0) cc_final: 0.6996 (p0) REVERT: E 493 CYS cc_start: 0.7665 (m) cc_final: 0.7222 (t) REVERT: F 108 MET cc_start: 0.7557 (mmp) cc_final: 0.6627 (ttm) outliers start: 27 outliers final: 8 residues processed: 334 average time/residue: 0.3365 time to fit residues: 174.1769 Evaluate side-chains 234 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 53 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 250 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 427 ASN ** A 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 285 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 GLN D 574 GLN D 702 ASN ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN E 578 HIS F 112 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22621 Z= 0.215 Angle : 0.642 11.795 30639 Z= 0.325 Chirality : 0.042 0.181 3528 Planarity : 0.004 0.066 3878 Dihedral : 5.292 77.054 2987 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.72 % Allowed : 16.21 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.07 (0.16), residues: 2790 helix: 1.73 (0.15), residues: 1076 sheet: -0.06 (0.22), residues: 565 loop : -1.57 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 525 HIS 0.017 0.001 HIS A 425 PHE 0.017 0.002 PHE E 557 TYR 0.017 0.002 TYR A 247 ARG 0.005 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8457 (tp40) cc_final: 0.7829 (pm20) REVERT: A 279 MET cc_start: 0.5471 (pmm) cc_final: 0.4798 (mtm) REVERT: A 699 LYS cc_start: 0.7350 (mppt) cc_final: 0.6806 (mppt) REVERT: A 770 MET cc_start: 0.7751 (ttm) cc_final: 0.7496 (ttm) REVERT: A 895 THR cc_start: 0.6950 (m) cc_final: 0.6731 (p) REVERT: B 171 MET cc_start: 0.6821 (tpp) cc_final: 0.5455 (tmm) REVERT: B 295 LEU cc_start: 0.3811 (OUTLIER) cc_final: 0.3528 (tp) REVERT: B 443 TRP cc_start: 0.6230 (m100) cc_final: 0.5659 (m100) REVERT: B 474 LEU cc_start: 0.8385 (mm) cc_final: 0.8054 (mt) REVERT: D 122 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4627 (mmt) REVERT: D 137 GLN cc_start: 0.6748 (tm-30) cc_final: 0.6523 (tm-30) REVERT: D 366 PHE cc_start: 0.5828 (m-10) cc_final: 0.5618 (m-80) REVERT: D 401 MET cc_start: 0.4387 (mtt) cc_final: 0.4136 (mtm) REVERT: D 440 TYR cc_start: 0.7805 (m-80) cc_final: 0.7515 (m-10) REVERT: D 487 ARG cc_start: 0.7286 (ptp-170) cc_final: 0.6982 (ptp-170) REVERT: D 553 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.5964 (mm-40) REVERT: D 565 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: D 622 LYS cc_start: 0.5775 (tppt) cc_final: 0.5455 (tttp) REVERT: D 657 MET cc_start: 0.7676 (tpt) cc_final: 0.7468 (tpt) REVERT: D 668 SER cc_start: 0.8007 (t) cc_final: 0.7750 (t) REVERT: D 680 GLU cc_start: 0.3164 (mp0) cc_final: 0.2045 (tt0) REVERT: D 744 MET cc_start: 0.7854 (mpp) cc_final: 0.7326 (mtt) REVERT: D 854 ASP cc_start: 0.7418 (p0) cc_final: 0.6714 (t0) REVERT: D 1021 GLU cc_start: 0.6360 (mm-30) cc_final: 0.5666 (mt-10) REVERT: E 171 MET cc_start: 0.6622 (ppp) cc_final: 0.6404 (ppp) REVERT: E 439 ASP cc_start: 0.7603 (p0) cc_final: 0.7027 (p0) REVERT: E 493 CYS cc_start: 0.7599 (m) cc_final: 0.7030 (t) REVERT: F 108 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6424 (ttm) outliers start: 68 outliers final: 37 residues processed: 288 average time/residue: 0.3047 time to fit residues: 142.9498 Evaluate side-chains 263 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 470 PHE Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 108 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 0.0020 chunk 248 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 201 optimal weight: 0.0670 overall best weight: 1.1930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS A 697 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN E 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22621 Z= 0.194 Angle : 0.599 11.652 30639 Z= 0.302 Chirality : 0.041 0.196 3528 Planarity : 0.004 0.051 3878 Dihedral : 4.801 57.913 2975 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.68 % Allowed : 17.85 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.16), residues: 2790 helix: 1.76 (0.15), residues: 1072 sheet: -0.17 (0.22), residues: 567 loop : -1.63 (0.17), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 525 HIS 0.015 0.001 HIS A 425 PHE 0.017 0.001 PHE E 557 TYR 0.021 0.002 TYR D 251 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 227 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8488 (tp40) cc_final: 0.7890 (pm20) REVERT: A 101 TYR cc_start: 0.6673 (t80) cc_final: 0.6256 (t80) REVERT: A 184 TRP cc_start: 0.7892 (p90) cc_final: 0.7475 (p90) REVERT: A 279 MET cc_start: 0.5518 (pmm) cc_final: 0.5154 (mtm) REVERT: A 393 MET cc_start: 0.8468 (ptp) cc_final: 0.8218 (ptm) REVERT: A 688 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5690 (tt) REVERT: A 699 LYS cc_start: 0.7337 (mppt) cc_final: 0.6778 (mppt) REVERT: A 770 MET cc_start: 0.7728 (ttm) cc_final: 0.7454 (ttm) REVERT: B 311 CYS cc_start: 0.8324 (m) cc_final: 0.7706 (p) REVERT: B 443 TRP cc_start: 0.6388 (m100) cc_final: 0.5740 (m100) REVERT: B 472 MET cc_start: 0.6707 (mpp) cc_final: 0.6188 (mpp) REVERT: D 122 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4606 (mmt) REVERT: D 137 GLN cc_start: 0.6641 (tm-30) cc_final: 0.6367 (tm-30) REVERT: D 251 TYR cc_start: 0.5959 (t80) cc_final: 0.5758 (t80) REVERT: D 366 PHE cc_start: 0.5866 (m-10) cc_final: 0.5640 (m-80) REVERT: D 425 HIS cc_start: 0.7889 (m170) cc_final: 0.7632 (m170) REVERT: D 440 TYR cc_start: 0.7734 (m-80) cc_final: 0.7446 (m-10) REVERT: D 487 ARG cc_start: 0.7249 (ptp-170) cc_final: 0.6822 (ptt-90) REVERT: D 565 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: D 668 SER cc_start: 0.8065 (t) cc_final: 0.7705 (p) REVERT: D 744 MET cc_start: 0.7458 (mpp) cc_final: 0.6765 (mtt) REVERT: D 834 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6681 (tt) REVERT: D 854 ASP cc_start: 0.7444 (p0) cc_final: 0.6695 (t0) REVERT: D 919 MET cc_start: 0.6298 (tmm) cc_final: 0.5748 (tmm) REVERT: D 1007 CYS cc_start: 0.7523 (m) cc_final: 0.7168 (t) REVERT: D 1021 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5589 (mt-10) REVERT: E 491 GLN cc_start: 0.6018 (tt0) cc_final: 0.5223 (tm-30) REVERT: E 567 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7028 (mm) REVERT: F 108 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6394 (ttm) outliers start: 92 outliers final: 49 residues processed: 299 average time/residue: 0.2850 time to fit residues: 140.4242 Evaluate side-chains 263 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 208 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 266 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 238 optimal weight: 0.0870 chunk 71 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 293 GLN B 383 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22621 Z= 0.141 Angle : 0.567 12.345 30639 Z= 0.280 Chirality : 0.040 0.183 3528 Planarity : 0.003 0.043 3878 Dihedral : 4.477 56.124 2974 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 19.50 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.16), residues: 2790 helix: 1.92 (0.16), residues: 1072 sheet: -0.15 (0.22), residues: 570 loop : -1.60 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 525 HIS 0.015 0.001 HIS A 425 PHE 0.019 0.001 PHE E 557 TYR 0.018 0.001 TYR D 251 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 233 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8530 (tp40) cc_final: 0.7979 (pm20) REVERT: A 101 TYR cc_start: 0.6832 (t80) cc_final: 0.6516 (t80) REVERT: A 184 TRP cc_start: 0.8095 (p90) cc_final: 0.7752 (p90) REVERT: A 200 ASP cc_start: 0.4863 (OUTLIER) cc_final: 0.4461 (p0) REVERT: A 699 LYS cc_start: 0.7392 (mppt) cc_final: 0.6807 (mppt) REVERT: A 770 MET cc_start: 0.7632 (ttm) cc_final: 0.7335 (ttm) REVERT: B 311 CYS cc_start: 0.8246 (m) cc_final: 0.7672 (p) REVERT: B 443 TRP cc_start: 0.6375 (m100) cc_final: 0.5732 (m100) REVERT: B 472 MET cc_start: 0.6689 (mpp) cc_final: 0.6107 (mpp) REVERT: D 122 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4639 (mmt) REVERT: D 251 TYR cc_start: 0.6011 (t80) cc_final: 0.5677 (t80) REVERT: D 273 LEU cc_start: 0.7028 (tp) cc_final: 0.6366 (tt) REVERT: D 366 PHE cc_start: 0.5834 (m-10) cc_final: 0.5608 (m-80) REVERT: D 425 HIS cc_start: 0.7913 (m170) cc_final: 0.7651 (m170) REVERT: D 487 ARG cc_start: 0.7198 (ptp-170) cc_final: 0.6850 (ptp-170) REVERT: D 553 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.5722 (mm-40) REVERT: D 565 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: D 668 SER cc_start: 0.8139 (t) cc_final: 0.7773 (p) REVERT: D 720 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5713 (mm) REVERT: D 854 ASP cc_start: 0.7431 (p0) cc_final: 0.6699 (t0) REVERT: D 1007 CYS cc_start: 0.7473 (m) cc_final: 0.7188 (t) REVERT: D 1021 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5395 (mt-10) REVERT: E 491 GLN cc_start: 0.5870 (tt0) cc_final: 0.5114 (tm-30) REVERT: E 567 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7028 (mm) REVERT: F 108 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6311 (ttm) outliers start: 84 outliers final: 49 residues processed: 297 average time/residue: 0.3072 time to fit residues: 148.8295 Evaluate side-chains 267 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 4.9990 chunk 151 optimal weight: 0.0870 chunk 3 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 383 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22621 Z= 0.207 Angle : 0.609 12.470 30639 Z= 0.304 Chirality : 0.041 0.211 3528 Planarity : 0.004 0.040 3878 Dihedral : 4.639 57.157 2973 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.40 % Allowed : 19.18 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.16), residues: 2790 helix: 1.75 (0.16), residues: 1077 sheet: -0.34 (0.22), residues: 558 loop : -1.65 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 525 HIS 0.011 0.001 HIS A 425 PHE 0.022 0.001 PHE E 557 TYR 0.015 0.002 TYR D 440 ARG 0.004 0.000 ARG D 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 218 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8546 (tp40) cc_final: 0.8054 (pm20) REVERT: A 101 TYR cc_start: 0.6810 (t80) cc_final: 0.6486 (t80) REVERT: A 184 TRP cc_start: 0.8279 (p90) cc_final: 0.7672 (p90) REVERT: A 200 ASP cc_start: 0.4834 (OUTLIER) cc_final: 0.4413 (p0) REVERT: A 426 MET cc_start: 0.6875 (tmm) cc_final: 0.6564 (tmm) REVERT: A 643 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7202 (mttm) REVERT: A 688 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5728 (tt) REVERT: A 699 LYS cc_start: 0.7522 (mppt) cc_final: 0.6887 (mppt) REVERT: A 770 MET cc_start: 0.7668 (ttm) cc_final: 0.7394 (ttm) REVERT: B 443 TRP cc_start: 0.6376 (m100) cc_final: 0.5728 (m100) REVERT: B 472 MET cc_start: 0.6729 (mpp) cc_final: 0.6099 (mpp) REVERT: D 122 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4686 (mmt) REVERT: D 137 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6701 (tm-30) REVERT: D 273 LEU cc_start: 0.6951 (tp) cc_final: 0.6235 (tt) REVERT: D 366 PHE cc_start: 0.5895 (m-10) cc_final: 0.5667 (m-80) REVERT: D 425 HIS cc_start: 0.8125 (m170) cc_final: 0.7865 (m170) REVERT: D 440 TYR cc_start: 0.7595 (m-80) cc_final: 0.7205 (m-10) REVERT: D 487 ARG cc_start: 0.7417 (ptp-170) cc_final: 0.7137 (ptp-170) REVERT: D 565 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6431 (m-80) REVERT: D 668 SER cc_start: 0.8179 (t) cc_final: 0.7808 (p) REVERT: D 720 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5746 (mm) REVERT: D 854 ASP cc_start: 0.7473 (p0) cc_final: 0.6587 (t0) REVERT: D 1007 CYS cc_start: 0.7470 (m) cc_final: 0.7169 (t) REVERT: D 1021 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5331 (mt-10) REVERT: E 567 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7097 (mm) REVERT: F 108 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6404 (ttm) outliers start: 110 outliers final: 74 residues processed: 306 average time/residue: 0.3128 time to fit residues: 156.1321 Evaluate side-chains 288 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 206 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 TRP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 267 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 383 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22621 Z= 0.148 Angle : 0.573 13.542 30639 Z= 0.285 Chirality : 0.040 0.197 3528 Planarity : 0.003 0.043 3878 Dihedral : 4.498 56.105 2973 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.28 % Allowed : 19.54 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.06 (0.16), residues: 2790 helix: 1.91 (0.16), residues: 1071 sheet: -0.24 (0.22), residues: 564 loop : -1.67 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 525 HIS 0.017 0.001 HIS A 425 PHE 0.019 0.001 PHE B 278 TYR 0.021 0.001 TYR D 251 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 223 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8560 (tp40) cc_final: 0.8083 (pm20) REVERT: A 101 TYR cc_start: 0.6767 (t80) cc_final: 0.6435 (t80) REVERT: A 184 TRP cc_start: 0.8233 (p90) cc_final: 0.7739 (p90) REVERT: A 200 ASP cc_start: 0.4850 (OUTLIER) cc_final: 0.4424 (p0) REVERT: A 426 MET cc_start: 0.6871 (tmm) cc_final: 0.6597 (tmm) REVERT: A 688 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5640 (tt) REVERT: A 699 LYS cc_start: 0.7488 (mppt) cc_final: 0.6874 (mppt) REVERT: A 770 MET cc_start: 0.7652 (ttm) cc_final: 0.7370 (ttm) REVERT: B 443 TRP cc_start: 0.6386 (m100) cc_final: 0.5720 (m100) REVERT: B 472 MET cc_start: 0.6578 (mpp) cc_final: 0.5878 (mpp) REVERT: D 122 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4826 (mmt) REVERT: D 137 GLN cc_start: 0.6866 (tm-30) cc_final: 0.6634 (tm-30) REVERT: D 216 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6404 (mt) REVERT: D 273 LEU cc_start: 0.7003 (tp) cc_final: 0.6275 (tt) REVERT: D 366 PHE cc_start: 0.5865 (m-10) cc_final: 0.5640 (m-80) REVERT: D 425 HIS cc_start: 0.8018 (m170) cc_final: 0.7753 (m170) REVERT: D 487 ARG cc_start: 0.7317 (ptp-170) cc_final: 0.7041 (ptp-170) REVERT: D 553 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5866 (mm-40) REVERT: D 565 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: D 668 SER cc_start: 0.8189 (t) cc_final: 0.7819 (p) REVERT: D 720 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5735 (mm) REVERT: D 854 ASP cc_start: 0.7444 (p0) cc_final: 0.6597 (t0) REVERT: D 1007 CYS cc_start: 0.7479 (m) cc_final: 0.7234 (t) REVERT: D 1021 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5329 (mt-10) REVERT: E 491 GLN cc_start: 0.5878 (tt0) cc_final: 0.5145 (tt0) REVERT: E 567 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7037 (mm) REVERT: F 108 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6189 (ttm) REVERT: F 111 TRP cc_start: 0.7337 (t60) cc_final: 0.7021 (t60) outliers start: 107 outliers final: 75 residues processed: 308 average time/residue: 0.2908 time to fit residues: 146.6159 Evaluate side-chains 291 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 207 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 892 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 383 GLN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 247 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 834 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 152 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 0.0770 chunk 224 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN B 292 HIS B 323 ASN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22621 Z= 0.192 Angle : 0.609 13.396 30639 Z= 0.300 Chirality : 0.041 0.220 3528 Planarity : 0.003 0.043 3878 Dihedral : 4.597 56.293 2973 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.64 % Allowed : 19.54 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.16), residues: 2790 helix: 1.81 (0.16), residues: 1074 sheet: -0.40 (0.22), residues: 554 loop : -1.72 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 525 HIS 0.014 0.001 HIS A 425 PHE 0.017 0.001 PHE D 173 TYR 0.030 0.002 TYR D 251 ARG 0.003 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 217 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8563 (tp40) cc_final: 0.8104 (pm20) REVERT: A 101 TYR cc_start: 0.6688 (t80) cc_final: 0.6374 (t80) REVERT: A 164 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: A 184 TRP cc_start: 0.8346 (p90) cc_final: 0.7822 (p90) REVERT: A 200 ASP cc_start: 0.4856 (OUTLIER) cc_final: 0.4426 (p0) REVERT: A 643 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7225 (mttm) REVERT: A 688 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5656 (tt) REVERT: A 699 LYS cc_start: 0.7495 (mppt) cc_final: 0.6877 (mppt) REVERT: A 770 MET cc_start: 0.7717 (ttm) cc_final: 0.7436 (ttm) REVERT: B 443 TRP cc_start: 0.6421 (m100) cc_final: 0.5763 (m100) REVERT: B 472 MET cc_start: 0.6645 (mpp) cc_final: 0.5938 (mpp) REVERT: D 122 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4626 (mmt) REVERT: D 216 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6570 (mt) REVERT: D 366 PHE cc_start: 0.5852 (m-10) cc_final: 0.5623 (m-80) REVERT: D 425 HIS cc_start: 0.8096 (m170) cc_final: 0.7853 (m170) REVERT: D 553 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.5974 (mm-40) REVERT: D 565 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: D 668 SER cc_start: 0.8243 (t) cc_final: 0.7925 (p) REVERT: D 720 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5758 (mm) REVERT: D 781 MET cc_start: 0.6473 (ppp) cc_final: 0.6044 (ppp) REVERT: D 863 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7985 (tt) REVERT: D 939 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6597 (ptmm) REVERT: D 1007 CYS cc_start: 0.7489 (m) cc_final: 0.7252 (t) REVERT: D 1021 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5715 (tt0) REVERT: E 471 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6457 (mm) REVERT: E 491 GLN cc_start: 0.5895 (tt0) cc_final: 0.5127 (tt0) REVERT: E 567 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7183 (mm) REVERT: F 108 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6345 (ttm) REVERT: F 111 TRP cc_start: 0.7401 (t60) cc_final: 0.7111 (t60) outliers start: 116 outliers final: 81 residues processed: 310 average time/residue: 0.3039 time to fit residues: 153.6105 Evaluate side-chains 301 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 206 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 892 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 80 optimal weight: 0.0000 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22621 Z= 0.148 Angle : 0.596 14.009 30639 Z= 0.290 Chirality : 0.040 0.195 3528 Planarity : 0.003 0.046 3878 Dihedral : 4.450 55.127 2973 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.92 % Allowed : 20.66 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.16), residues: 2790 helix: 1.95 (0.16), residues: 1069 sheet: -0.31 (0.22), residues: 566 loop : -1.67 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 525 HIS 0.024 0.001 HIS A 425 PHE 0.015 0.001 PHE E 557 TYR 0.026 0.001 TYR D 251 ARG 0.003 0.000 ARG D 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 225 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8565 (tp40) cc_final: 0.8108 (pm20) REVERT: A 184 TRP cc_start: 0.8340 (p90) cc_final: 0.7809 (p90) REVERT: A 200 ASP cc_start: 0.4829 (OUTLIER) cc_final: 0.4379 (p0) REVERT: A 426 MET cc_start: 0.6906 (tmm) cc_final: 0.6642 (tmm) REVERT: A 688 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5593 (tt) REVERT: A 770 MET cc_start: 0.7655 (ttm) cc_final: 0.7365 (ttm) REVERT: A 964 LYS cc_start: 0.7679 (tmmt) cc_final: 0.7282 (pptt) REVERT: B 323 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6736 (p0) REVERT: B 443 TRP cc_start: 0.6398 (m100) cc_final: 0.5761 (m100) REVERT: B 472 MET cc_start: 0.6652 (mpp) cc_final: 0.5917 (mpp) REVERT: D 122 MET cc_start: 0.5347 (OUTLIER) cc_final: 0.4838 (tpp) REVERT: D 216 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.5902 (mp) REVERT: D 366 PHE cc_start: 0.5827 (m-10) cc_final: 0.5604 (m-80) REVERT: D 425 HIS cc_start: 0.8196 (m170) cc_final: 0.7964 (m170) REVERT: D 553 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6139 (mm-40) REVERT: D 565 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6377 (m-80) REVERT: D 668 SER cc_start: 0.8312 (t) cc_final: 0.7937 (p) REVERT: D 720 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5739 (mm) REVERT: D 781 MET cc_start: 0.6511 (ppp) cc_final: 0.6080 (ppp) REVERT: D 939 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6668 (ptmm) REVERT: D 1021 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5661 (tt0) REVERT: E 491 GLN cc_start: 0.5831 (tt0) cc_final: 0.5076 (tt0) REVERT: E 567 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7143 (mm) REVERT: F 108 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6268 (ttm) outliers start: 98 outliers final: 76 residues processed: 301 average time/residue: 0.2986 time to fit residues: 145.8364 Evaluate side-chains 293 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 206 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 892 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 323 ASN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 553 GLN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 465 HIS ** B 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN F 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22621 Z= 0.262 Angle : 0.686 13.847 30639 Z= 0.338 Chirality : 0.043 0.239 3528 Planarity : 0.004 0.040 3878 Dihedral : 4.857 57.301 2973 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.64 % Allowed : 20.42 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.34 (0.16), residues: 2790 helix: 1.51 (0.16), residues: 1084 sheet: -0.51 (0.22), residues: 540 loop : -1.80 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 525 HIS 0.021 0.002 HIS A 425 PHE 0.019 0.002 PHE B 278 TYR 0.025 0.002 TYR A 101 ARG 0.004 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 209 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8626 (tp40) cc_final: 0.8147 (pm20) REVERT: A 184 TRP cc_start: 0.8316 (p90) cc_final: 0.7652 (p90) REVERT: A 200 ASP cc_start: 0.4436 (OUTLIER) cc_final: 0.3740 (p0) REVERT: A 469 CYS cc_start: 0.7385 (t) cc_final: 0.7163 (p) REVERT: A 688 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5522 (tt) REVERT: A 770 MET cc_start: 0.7652 (ttm) cc_final: 0.7373 (ttm) REVERT: B 443 TRP cc_start: 0.6502 (m100) cc_final: 0.5756 (m100) REVERT: B 472 MET cc_start: 0.6743 (mpp) cc_final: 0.5961 (mpp) REVERT: B 474 LEU cc_start: 0.8329 (mm) cc_final: 0.8087 (mt) REVERT: D 122 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4706 (mmt) REVERT: D 216 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6357 (mp) REVERT: D 366 PHE cc_start: 0.5907 (m-10) cc_final: 0.5674 (m-80) REVERT: D 425 HIS cc_start: 0.8266 (m170) cc_final: 0.8013 (m170) REVERT: D 565 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: D 668 SER cc_start: 0.8354 (t) cc_final: 0.7975 (p) REVERT: D 720 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5840 (mm) REVERT: D 781 MET cc_start: 0.6423 (ppp) cc_final: 0.5882 (ppp) REVERT: D 939 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6719 (ptmm) REVERT: D 1021 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5787 (tt0) REVERT: E 442 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6618 (mp) REVERT: E 567 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (mm) REVERT: F 108 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6309 (ttm) outliers start: 116 outliers final: 92 residues processed: 302 average time/residue: 0.3192 time to fit residues: 158.8356 Evaluate side-chains 306 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 204 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 892 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 279 MET Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 854 ASP Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 442 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 572 ASP Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 218 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 134 optimal weight: 0.1980 chunk 173 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS D 137 GLN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22621 Z= 0.151 Angle : 0.628 14.530 30639 Z= 0.304 Chirality : 0.040 0.228 3528 Planarity : 0.003 0.043 3878 Dihedral : 4.569 55.496 2973 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.84 % Allowed : 21.18 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.12 (0.16), residues: 2790 helix: 1.78 (0.16), residues: 1072 sheet: -0.40 (0.22), residues: 562 loop : -1.75 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 525 HIS 0.021 0.001 HIS A 425 PHE 0.015 0.001 PHE D 173 TYR 0.030 0.001 TYR D 251 ARG 0.002 0.000 ARG D 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 214 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8618 (tp40) cc_final: 0.8140 (pm20) REVERT: A 184 TRP cc_start: 0.8237 (p90) cc_final: 0.7643 (p90) REVERT: A 200 ASP cc_start: 0.4239 (OUTLIER) cc_final: 0.3558 (p0) REVERT: A 426 MET cc_start: 0.6864 (tmm) cc_final: 0.6589 (tmm) REVERT: A 688 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5523 (tt) REVERT: A 770 MET cc_start: 0.7662 (ttm) cc_final: 0.7360 (ttm) REVERT: A 964 LYS cc_start: 0.7469 (tmmt) cc_final: 0.7056 (pptt) REVERT: B 443 TRP cc_start: 0.6433 (m100) cc_final: 0.5717 (m100) REVERT: B 472 MET cc_start: 0.6715 (mpp) cc_final: 0.6353 (mpp) REVERT: B 474 LEU cc_start: 0.8322 (mm) cc_final: 0.8068 (mt) REVERT: C 101 MET cc_start: 0.1299 (tpp) cc_final: 0.0881 (mpp) REVERT: D 122 MET cc_start: 0.5251 (OUTLIER) cc_final: 0.4701 (mmt) REVERT: D 216 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6197 (mt) REVERT: D 366 PHE cc_start: 0.5850 (m-10) cc_final: 0.5626 (m-80) REVERT: D 425 HIS cc_start: 0.8322 (m170) cc_final: 0.8108 (m170) REVERT: D 565 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: D 668 SER cc_start: 0.8359 (t) cc_final: 0.8000 (p) REVERT: D 720 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5787 (mm) REVERT: D 781 MET cc_start: 0.6417 (ppp) cc_final: 0.5996 (ppp) REVERT: D 939 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6780 (ptmm) REVERT: D 1021 GLU cc_start: 0.5956 (mm-30) cc_final: 0.5704 (tt0) REVERT: E 491 GLN cc_start: 0.5820 (tt0) cc_final: 0.5059 (tt0) REVERT: E 567 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7222 (mm) REVERT: F 108 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6283 (ttm) outliers start: 96 outliers final: 81 residues processed: 288 average time/residue: 0.3214 time to fit residues: 149.9924 Evaluate side-chains 298 residues out of total 2524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 208 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 743 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 892 LYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 112 HIS Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 324 PHE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 594 ILE Chi-restraints excluded: chain D residue 601 LEU Chi-restraints excluded: chain D residue 661 CYS Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 757 CYS Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 854 ASP Chi-restraints excluded: chain D residue 911 ASN Chi-restraints excluded: chain D residue 939 LYS Chi-restraints excluded: chain D residue 943 THR Chi-restraints excluded: chain D residue 966 THR Chi-restraints excluded: chain D residue 968 ASN Chi-restraints excluded: chain D residue 1017 LEU Chi-restraints excluded: chain E residue 156 GLN Chi-restraints excluded: chain E residue 259 GLU Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 328 ASP Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 473 SER Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 512 THR Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 528 VAL Chi-restraints excluded: chain E residue 567 ILE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS D 137 GLN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 848 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1011 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.181620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.144844 restraints weight = 39082.992| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.06 r_work: 0.4182 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22621 Z= 0.178 Angle : 0.635 14.389 30639 Z= 0.309 Chirality : 0.041 0.242 3528 Planarity : 0.003 0.044 3878 Dihedral : 4.589 55.654 2973 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.80 % Allowed : 21.38 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.19 (0.16), residues: 2790 helix: 1.72 (0.16), residues: 1072 sheet: -0.51 (0.22), residues: 552 loop : -1.74 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 525 HIS 0.020 0.001 HIS A 425 PHE 0.016 0.001 PHE D 173 TYR 0.016 0.001 TYR D 247 ARG 0.002 0.000 ARG E 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4961.60 seconds wall clock time: 90 minutes 49.48 seconds (5449.48 seconds total)