Starting phenix.real_space_refine on Thu Jul 25 02:56:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jj1_36337/07_2024/8jj1_36337.cif" } resolution = 3.77 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= 0.003 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 158 5.16 5 C 17933 2.51 5 N 4689 2.21 5 O 5246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28026 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "A" Number of atoms: 6033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6033 Classifications: {'peptide': 763} Link IDs: {'PTRANS': 31, 'TRANS': 731} Chain breaks: 5 Chain: "B" Number of atoms: 6153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 6153 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 745} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6004 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 730} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 6158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6158 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.57, per 1000 atoms: 0.56 Number of scatterers: 28026 At special positions: 0 Unit cell: (167.4, 177.12, 176.04, 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 158 16.00 O 5246 8.00 N 4689 7.00 C 17933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 276 " " NAG B 902 " - " ASN B 368 " " NAG B 903 " - " ASN B 350 " " NAG B 904 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 368 " " NAG D 904 " - " ASN D 350 " " NAG D 905 " - " ASN D 771 " " NAG I 1 " - " ASN B 61 " Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 4.6 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6592 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 33 sheets defined 38.6% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.708A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 59 removed outlier: 3.504A pdb=" N ARG A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.958A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.771A pdb=" N MET A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.735A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.085A pdb=" N PHE A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 232 through 247 Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.159A pdb=" N VAL A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.959A pdb=" N THR A 382 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.870A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 579 removed outlier: 4.200A pdb=" N LEU A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.818A pdb=" N LEU A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 651 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 706 Processing helix chain 'A' and resid 707 through 709 No H-bonds generated for 'chain 'A' and resid 707 through 709' Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.519A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 771 through 785 removed outlier: 3.752A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 Processing helix chain 'B' and resid 35 through 51 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.683A pdb=" N THR B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 3.758A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP B 130 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.857A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.645A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.593A pdb=" N HIS B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 582 removed outlier: 3.766A pdb=" N LEU B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 582 " --> pdb=" O TYR B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 Processing helix chain 'B' and resid 627 through 656 removed outlier: 3.509A pdb=" N VAL B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.958A pdb=" N HIS B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 812 through 840 removed outlier: 3.545A pdb=" N PHE B 817 " --> pdb=" O MET B 813 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B 832 " --> pdb=" O ILE B 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.987A pdb=" N ARG C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.536A pdb=" N ALA C 60 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.893A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.620A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.884A pdb=" N PHE C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.995A pdb=" N SER C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.893A pdb=" N VAL C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 560 through 579 removed outlier: 3.708A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 613 removed outlier: 4.209A pdb=" N ILE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE C 613 " --> pdb=" O TRP C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 632 Processing helix chain 'C' and resid 633 through 653 removed outlier: 4.109A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.575A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.772A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 707 through 709 No H-bonds generated for 'chain 'C' and resid 707 through 709' Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 742 Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.175A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 removed outlier: 3.733A pdb=" N LEU C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 837 removed outlier: 3.719A pdb=" N MET C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 104 through 114 removed outlier: 3.559A pdb=" N THR D 110 " --> pdb=" O PRO D 106 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.033A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 removed outlier: 3.935A pdb=" N GLU D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 276 through 299 removed outlier: 3.525A pdb=" N HIS D 280 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 583 removed outlier: 4.262A pdb=" N LEU D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 654 removed outlier: 3.711A pdb=" N TRP D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA D 637 " --> pdb=" O GLY D 633 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.906A pdb=" N ASP D 658 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG D 659 " --> pdb=" O VAL D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 655 through 659' Processing helix chain 'D' and resid 669 through 674 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.563A pdb=" N HIS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 769 through 782 removed outlier: 3.594A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 837 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.713A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.700A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 94 No H-bonds generated for 'chain 'G' and resid 92 through 94' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.674A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 73 removed outlier: 7.184A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 removed outlier: 3.681A pdb=" N VAL A 173 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 227 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.896A pdb=" N MET A 507 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 409 " --> pdb=" O MET A 507 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 418 through 420 removed outlier: 3.545A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 731 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 66 removed outlier: 6.279A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.378A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP B 247 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU B 269 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 249 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N LEU B 271 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 478 removed outlier: 3.905A pdb=" N MET B 512 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.783A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 534 through 536 removed outlier: 4.077A pdb=" N LYS B 534 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 682 removed outlier: 6.972A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.576A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.574A pdb=" N TRP C 255 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 279 " --> pdb=" O TRP C 255 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL C 257 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 363 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 446 through 456 removed outlier: 8.516A pdb=" N GLU C 448 " --> pdb=" O ILE C 442 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE C 442 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 477 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE C 439 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 407 " --> pdb=" O MET C 507 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AC2, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.299A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.445A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU D 119 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.618A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP D 247 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU D 269 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL D 249 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU D 271 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 266 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 351 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE D 366 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 353 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 329 through 330 Processing sheet with id=AC6, first strand: chain 'D' and resid 397 through 402 removed outlier: 6.375A pdb=" N LEU D 398 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS D 477 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 400 " --> pdb=" O HIS D 477 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE D 435 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LEU D 478 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 512 through 515 removed outlier: 4.874A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 681 through 682 removed outlier: 3.564A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.551A pdb=" N ARG E 98 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.989A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 removed outlier: 7.014A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 1206 hydrogen bonds defined for protein. 3399 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: 10.34 Time building geometry restraints manager: 11.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8950 1.34 - 1.46: 6892 1.46 - 1.58: 12562 1.58 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 28676 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" CA GLN D 686 " pdb=" CB GLN D 686 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.21e-02 6.83e+03 2.18e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 28671 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.97: 871 106.97 - 113.74: 15863 113.74 - 120.51: 10771 120.51 - 127.28: 11043 127.28 - 134.05: 355 Bond angle restraints: 38903 Sorted by residual: angle pdb=" N SER G 93 " pdb=" CA SER G 93 " pdb=" C SER G 93 " ideal model delta sigma weight residual 114.75 109.09 5.66 1.26e+00 6.30e-01 2.02e+01 angle pdb=" CA SER G 93 " pdb=" C SER G 93 " pdb=" N TYR G 94 " ideal model delta sigma weight residual 119.80 115.98 3.82 1.34e+00 5.57e-01 8.15e+00 angle pdb=" CA SER G 93 " pdb=" C SER G 93 " pdb=" O SER G 93 " ideal model delta sigma weight residual 118.47 120.80 -2.33 1.14e+00 7.69e-01 4.17e+00 angle pdb=" N TYR C 286 " pdb=" CA TYR C 286 " pdb=" C TYR C 286 " ideal model delta sigma weight residual 108.34 111.01 -2.67 1.31e+00 5.83e-01 4.14e+00 angle pdb=" C THR D 550 " pdb=" N LEU D 551 " pdb=" CA LEU D 551 " ideal model delta sigma weight residual 121.54 125.42 -3.88 1.91e+00 2.74e-01 4.14e+00 ... (remaining 38898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 16378 17.51 - 35.02: 627 35.02 - 52.54: 151 52.54 - 70.05: 11 70.05 - 87.56: 8 Dihedral angle restraints: 17175 sinusoidal: 6942 harmonic: 10233 Sorted by residual: dihedral pdb=" CA LYS G 92 " pdb=" C LYS G 92 " pdb=" N SER G 93 " pdb=" CA SER G 93 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG D 52 " pdb=" CB ARG D 52 " pdb=" CG ARG D 52 " pdb=" CD ARG D 52 " ideal model delta sinusoidal sigma weight residual 180.00 120.47 59.53 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N GLN D 59 " pdb=" CA GLN D 59 " pdb=" CB GLN D 59 " pdb=" CG GLN D 59 " ideal model delta sinusoidal sigma weight residual 60.00 2.19 57.81 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 17172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3504 0.045 - 0.090: 609 0.090 - 0.135: 288 0.135 - 0.180: 1 0.180 - 0.225: 1 Chirality restraints: 4403 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 687 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1 NAG D 905 " pdb=" ND2 ASN D 771 " pdb=" C2 NAG D 905 " pdb=" O5 NAG D 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE B 546 " pdb=" N ILE B 546 " pdb=" C ILE B 546 " pdb=" CB ILE B 546 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 4400 not shown) Planarity restraints: 4923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 318 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 319 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 318 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 319 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 546 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO D 547 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 547 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 547 " 0.017 5.00e-02 4.00e+02 ... (remaining 4920 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3184 2.75 - 3.29: 28420 3.29 - 3.83: 47298 3.83 - 4.36: 53647 4.36 - 4.90: 93090 Nonbonded interactions: 225639 Sorted by model distance: nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.217 2.440 nonbonded pdb=" ND2 ASN B 70 " pdb=" O TYR C 321 " model vdw 2.220 2.520 nonbonded pdb=" OD2 ASP A 45 " pdb=" OG1 THR A 47 " model vdw 2.243 2.440 nonbonded pdb=" OD2 ASP B 283 " pdb=" OG1 THR B 335 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP D 417 " pdb=" OG1 THR D 419 " model vdw 2.249 2.440 ... (remaining 225634 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 34 through 540 or resid 546 through 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 625 through 837 or \ resid 901)) selection = (chain 'C' and (resid 34 through 540 or resid 546 through 796 or resid 813 throu \ gh 837 or resid 901)) } ncs_group { reference = (chain 'B' and (resid 25 through 658 or (resid 659 and (name N or name CA or nam \ e C or name O or name CB )) or resid 660 through 837 or resid 901 through 904)) selection = (chain 'D' and (resid 25 through 584 or resid 604 through 796 or resid 811 throu \ gh 837 or resid 902 through 905)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.340 Find NCS groups from input model: 2.250 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.002 0.037 28676 Z= 0.114 Angle : 0.411 7.015 38903 Z= 0.209 Chirality : 0.040 0.225 4403 Planarity : 0.003 0.034 4911 Dihedral : 9.548 87.562 10535 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 3.60 % Allowed : 7.59 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 1.29 (0.15), residues: 3489 helix: 2.29 (0.15), residues: 1216 sheet: 1.05 (0.23), residues: 604 loop : -0.30 (0.17), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 55 HIS 0.002 0.000 HIS B 134 PHE 0.012 0.001 PHE B 817 TYR 0.006 0.001 TYR A 281 ARG 0.001 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 420 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.7624 (mt) cc_final: 0.7299 (mm) REVERT: H 116 LEU cc_start: 0.8574 (tp) cc_final: 0.8118 (mp) REVERT: A 324 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6777 (mpp) REVERT: A 517 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: A 641 PHE cc_start: 0.3526 (OUTLIER) cc_final: 0.3301 (t80) REVERT: A 653 MET cc_start: 0.4402 (mtp) cc_final: 0.2376 (tpt) REVERT: A 828 MET cc_start: 0.3487 (tpt) cc_final: 0.3009 (tmm) REVERT: B 57 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7986 (tppt) REVERT: B 58 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 548 ARG cc_start: 0.2666 (mtm-85) cc_final: 0.1664 (tpt-90) REVERT: B 607 MET cc_start: 0.5317 (pp-130) cc_final: 0.4917 (tpp) REVERT: B 639 PHE cc_start: 0.7403 (t80) cc_final: 0.6835 (t80) REVERT: B 702 MET cc_start: 0.7183 (ppp) cc_final: 0.6154 (ppp) REVERT: C 39 MET cc_start: 0.7675 (mtp) cc_final: 0.7216 (mtp) REVERT: C 138 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7319 (mtmt) REVERT: C 252 ASP cc_start: 0.8059 (p0) cc_final: 0.7851 (p0) REVERT: C 475 TYR cc_start: 0.5038 (m-80) cc_final: 0.4500 (m-80) REVERT: C 560 MET cc_start: 0.2030 (ppp) cc_final: 0.1320 (ttm) REVERT: C 653 MET cc_start: 0.5870 (ppp) cc_final: 0.4512 (mmt) REVERT: D 354 MET cc_start: 0.7536 (mmm) cc_final: 0.7323 (mmm) REVERT: G 2 ILE cc_start: 0.6681 (mp) cc_final: 0.5956 (mm) outliers start: 110 outliers final: 24 residues processed: 512 average time/residue: 0.4174 time to fit residues: 323.5828 Evaluate side-chains 242 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 636 PHE Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 703 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 20.0000 chunk 266 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 179 optimal weight: 0.0980 chunk 142 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 0.0770 chunk 167 optimal weight: 7.9990 chunk 204 optimal weight: 0.0670 chunk 318 optimal weight: 4.9990 overall best weight: 1.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN A 671 GLN A 766 GLN B 48 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 270 GLN B 290 GLN B 293 HIS B 371 HIS B 477 HIS B 509 GLN B 521 ASN B 525 GLN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 812 ASN C 59 GLN C 152 GLN C 154 GLN C 380 ASN C 485 HIS C 490 ASN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 487 GLN D 521 ASN D 525 GLN D 556 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 37 GLN F 42 GLN F 55 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28676 Z= 0.178 Angle : 0.522 11.058 38903 Z= 0.267 Chirality : 0.043 0.272 4403 Planarity : 0.003 0.037 4911 Dihedral : 5.240 71.451 4127 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.39 % Rotamer: Outliers : 2.52 % Allowed : 11.62 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 1.13 (0.15), residues: 3489 helix: 2.14 (0.15), residues: 1230 sheet: 0.86 (0.22), residues: 621 loop : -0.36 (0.17), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 160 HIS 0.005 0.001 HIS A 44 PHE 0.035 0.001 PHE A 183 TYR 0.020 0.001 TYR H 110 ARG 0.005 0.000 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 219 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6782 (mpp) REVERT: A 507 MET cc_start: 0.8124 (ttm) cc_final: 0.7836 (mtp) REVERT: A 517 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: A 641 PHE cc_start: 0.3585 (OUTLIER) cc_final: 0.3373 (t80) REVERT: A 653 MET cc_start: 0.4506 (mtp) cc_final: 0.2362 (tpt) REVERT: A 697 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8447 (t0) REVERT: A 828 MET cc_start: 0.3613 (tpt) cc_final: 0.3097 (tmm) REVERT: B 57 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.7951 (tppt) REVERT: B 58 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8070 (pt) REVERT: B 154 MET cc_start: 0.8342 (mtp) cc_final: 0.8117 (mtp) REVERT: B 416 SER cc_start: 0.8447 (m) cc_final: 0.7505 (t) REVERT: B 548 ARG cc_start: 0.2815 (mtm-85) cc_final: 0.1666 (tpt-90) REVERT: B 607 MET cc_start: 0.5492 (pp-130) cc_final: 0.5038 (tpp) REVERT: B 639 PHE cc_start: 0.7309 (t80) cc_final: 0.6852 (t80) REVERT: B 702 MET cc_start: 0.7402 (ppp) cc_final: 0.6666 (ppp) REVERT: C 138 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7513 (mtmt) REVERT: C 162 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7735 (mtm) REVERT: C 252 ASP cc_start: 0.8046 (p0) cc_final: 0.7776 (p0) REVERT: C 331 MET cc_start: 0.2822 (ptm) cc_final: 0.1942 (ptm) REVERT: C 332 HIS cc_start: 0.5792 (t-90) cc_final: 0.5476 (t-90) REVERT: C 653 MET cc_start: 0.6123 (ppp) cc_final: 0.4681 (mmm) REVERT: D 354 MET cc_start: 0.7740 (mmm) cc_final: 0.7484 (mmm) REVERT: D 512 MET cc_start: 0.8240 (ttp) cc_final: 0.8037 (ttm) REVERT: G 2 ILE cc_start: 0.6607 (mp) cc_final: 0.5995 (pt) REVERT: G 42 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 77 outliers final: 26 residues processed: 286 average time/residue: 0.4113 time to fit residues: 186.8436 Evaluate side-chains 214 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 697 ASN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 319 optimal weight: 30.0000 chunk 344 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN B 38 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 293 HIS ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN D 521 ASN D 525 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28676 Z= 0.347 Angle : 0.631 10.365 38903 Z= 0.326 Chirality : 0.045 0.377 4403 Planarity : 0.004 0.057 4911 Dihedral : 5.441 72.909 4120 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 3.14 % Allowed : 11.55 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.67 (0.15), residues: 3489 helix: 1.74 (0.15), residues: 1231 sheet: 0.27 (0.22), residues: 626 loop : -0.45 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 609 HIS 0.009 0.001 HIS D 280 PHE 0.045 0.002 PHE D 42 TYR 0.024 0.002 TYR A 822 ARG 0.012 0.001 ARG E 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 193 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7632 (mp) REVERT: H 116 LEU cc_start: 0.8340 (tp) cc_final: 0.8004 (tt) REVERT: A 112 MET cc_start: 0.8601 (mmm) cc_final: 0.8336 (mmt) REVERT: A 134 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7756 (tt) REVERT: A 183 PHE cc_start: 0.5635 (m-80) cc_final: 0.4809 (m-80) REVERT: A 230 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5581 (t80) REVERT: A 306 MET cc_start: 0.7571 (ttt) cc_final: 0.7367 (tpp) REVERT: A 705 MET cc_start: 0.7159 (mmt) cc_final: 0.6804 (mmt) REVERT: A 828 MET cc_start: 0.3745 (tpt) cc_final: 0.3257 (ttp) REVERT: B 57 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.7924 (tppt) REVERT: B 58 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 72 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.7835 (mt) REVERT: B 341 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7698 (m-40) REVERT: B 470 MET cc_start: 0.8593 (mtm) cc_final: 0.8245 (mtm) REVERT: B 546 ILE cc_start: 0.5282 (OUTLIER) cc_final: 0.4383 (pt) REVERT: B 548 ARG cc_start: 0.3436 (mtm-85) cc_final: 0.1665 (tpt-90) REVERT: B 555 MET cc_start: 0.3596 (ptp) cc_final: 0.3245 (ptm) REVERT: B 607 MET cc_start: 0.5273 (pp-130) cc_final: 0.4825 (tpp) REVERT: B 639 PHE cc_start: 0.7264 (t80) cc_final: 0.6818 (t80) REVERT: B 702 MET cc_start: 0.7371 (ppp) cc_final: 0.6872 (ppp) REVERT: B 705 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6911 (p-80) REVERT: B 736 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 74 MET cc_start: 0.8522 (pmm) cc_final: 0.8127 (pmm) REVERT: C 138 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7512 (mtmt) REVERT: C 252 ASP cc_start: 0.8158 (p0) cc_final: 0.7856 (p0) REVERT: C 321 TYR cc_start: 0.5013 (OUTLIER) cc_final: 0.4783 (p90) REVERT: C 653 MET cc_start: 0.6108 (ppp) cc_final: 0.4979 (mmm) REVERT: D 354 MET cc_start: 0.7958 (mmm) cc_final: 0.7556 (mmm) REVERT: D 501 MET cc_start: 0.9181 (ttm) cc_final: 0.8977 (ttm) REVERT: G 42 GLN cc_start: 0.7690 (mt0) cc_final: 0.7439 (mp10) REVERT: G 50 MET cc_start: 0.7513 (mmm) cc_final: 0.7060 (mmm) outliers start: 96 outliers final: 40 residues processed: 276 average time/residue: 0.3842 time to fit residues: 171.3327 Evaluate side-chains 226 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 174 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 341 ASN Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 555 MET Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 703 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 303 optimal weight: 0.0070 chunk 91 optimal weight: 5.9990 overall best weight: 3.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 HIS ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN D 393 GLN D 499 ASN E 65 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28676 Z= 0.290 Angle : 0.583 12.612 38903 Z= 0.297 Chirality : 0.044 0.358 4403 Planarity : 0.004 0.039 4911 Dihedral : 5.002 48.154 4101 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.11 % Allowed : 13.00 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.53 (0.15), residues: 3489 helix: 1.67 (0.15), residues: 1233 sheet: 0.20 (0.22), residues: 611 loop : -0.57 (0.17), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 609 HIS 0.008 0.001 HIS D 280 PHE 0.049 0.002 PHE D 42 TYR 0.022 0.002 TYR H 32 ARG 0.006 0.001 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 178 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7939 (m-80) cc_final: 0.7735 (m-80) REVERT: H 116 LEU cc_start: 0.8337 (tp) cc_final: 0.7971 (tt) REVERT: A 134 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7953 (tt) REVERT: A 306 MET cc_start: 0.7644 (ttt) cc_final: 0.7342 (tpp) REVERT: A 324 MET cc_start: 0.8183 (mpp) cc_final: 0.7635 (mpp) REVERT: A 828 MET cc_start: 0.3604 (tpt) cc_final: 0.3077 (tmm) REVERT: B 58 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8416 (pt) REVERT: B 363 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8270 (tm130) REVERT: B 546 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.4483 (pt) REVERT: B 548 ARG cc_start: 0.3397 (mtm-85) cc_final: 0.1429 (tpt-90) REVERT: B 555 MET cc_start: 0.3570 (ptp) cc_final: 0.3229 (ptm) REVERT: B 607 MET cc_start: 0.5441 (pp-130) cc_final: 0.4885 (tpp) REVERT: B 639 PHE cc_start: 0.7438 (t80) cc_final: 0.6933 (t80) REVERT: B 702 MET cc_start: 0.7270 (ppp) cc_final: 0.6637 (ppp) REVERT: B 736 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 745 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (p0) REVERT: C 74 MET cc_start: 0.8584 (pmm) cc_final: 0.8111 (pmm) REVERT: C 138 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7647 (mttm) REVERT: C 170 PHE cc_start: 0.8537 (m-10) cc_final: 0.8336 (m-10) REVERT: C 252 ASP cc_start: 0.8182 (p0) cc_final: 0.7846 (p0) REVERT: C 653 MET cc_start: 0.6024 (ppp) cc_final: 0.5052 (mmm) REVERT: D 354 MET cc_start: 0.7935 (mmm) cc_final: 0.7547 (mmm) REVERT: D 501 MET cc_start: 0.9249 (ttm) cc_final: 0.8928 (ttm) REVERT: D 635 VAL cc_start: 0.4981 (OUTLIER) cc_final: 0.4691 (t) REVERT: D 706 MET cc_start: 0.8948 (mmm) cc_final: 0.8641 (mmp) REVERT: G 50 MET cc_start: 0.7619 (mmm) cc_final: 0.7174 (mmm) outliers start: 95 outliers final: 47 residues processed: 260 average time/residue: 0.3910 time to fit residues: 164.2389 Evaluate side-chains 218 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 647 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS D 280 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS E 65 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 28676 Z= 0.382 Angle : 0.638 13.046 38903 Z= 0.327 Chirality : 0.045 0.416 4403 Planarity : 0.004 0.099 4911 Dihedral : 5.218 54.768 4095 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 3.37 % Allowed : 13.26 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3489 helix: 1.50 (0.15), residues: 1239 sheet: -0.14 (0.22), residues: 621 loop : -0.72 (0.17), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 609 HIS 0.010 0.001 HIS D 280 PHE 0.049 0.002 PHE D 42 TYR 0.026 0.002 TYR A 165 ARG 0.013 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 171 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7978 (m-80) cc_final: 0.7730 (m-80) REVERT: H 116 LEU cc_start: 0.8416 (tp) cc_final: 0.8062 (tt) REVERT: A 181 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7456 (mmt-90) REVERT: A 324 MET cc_start: 0.8297 (mpp) cc_final: 0.7727 (mpp) REVERT: A 331 MET cc_start: 0.5692 (tmm) cc_final: 0.5460 (tmm) REVERT: A 392 ARG cc_start: 0.5715 (ptt-90) cc_final: 0.5445 (ptp90) REVERT: A 630 MET cc_start: 0.6840 (mtt) cc_final: 0.6609 (mtp) REVERT: A 828 MET cc_start: 0.3587 (tpt) cc_final: 0.3019 (tmm) REVERT: B 58 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8538 (pt) REVERT: B 546 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.4550 (pt) REVERT: B 548 ARG cc_start: 0.3432 (mtm-85) cc_final: 0.1088 (tpt-90) REVERT: B 555 MET cc_start: 0.3880 (ptp) cc_final: 0.3555 (ptm) REVERT: B 607 MET cc_start: 0.5374 (pp-130) cc_final: 0.4802 (tpp) REVERT: B 639 PHE cc_start: 0.7438 (t80) cc_final: 0.7052 (t80) REVERT: B 702 MET cc_start: 0.7386 (ppp) cc_final: 0.6722 (ppp) REVERT: B 736 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 74 MET cc_start: 0.8582 (pmm) cc_final: 0.8188 (pmm) REVERT: C 138 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7720 (mttm) REVERT: C 200 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8321 (tpt) REVERT: C 252 ASP cc_start: 0.8239 (p0) cc_final: 0.7812 (p0) REVERT: C 653 MET cc_start: 0.6036 (ppp) cc_final: 0.5091 (mmm) REVERT: D 354 MET cc_start: 0.7899 (mmm) cc_final: 0.7515 (mmm) REVERT: D 501 MET cc_start: 0.9272 (ttm) cc_final: 0.8932 (ttm) REVERT: D 607 MET cc_start: 0.5985 (ptt) cc_final: 0.5628 (ppp) REVERT: D 706 MET cc_start: 0.8966 (mmm) cc_final: 0.8667 (mmp) REVERT: F 58 VAL cc_start: 0.6203 (t) cc_final: 0.5930 (t) REVERT: G 39 ARG cc_start: 0.7717 (mpp-170) cc_final: 0.6917 (mmt90) REVERT: G 42 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: G 50 MET cc_start: 0.7813 (mmm) cc_final: 0.7432 (mmm) outliers start: 103 outliers final: 62 residues processed: 256 average time/residue: 0.3790 time to fit residues: 158.0025 Evaluate side-chains 229 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 160 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 555 MET Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 3.9990 chunk 305 optimal weight: 0.1980 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 157 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 GLN B 650 ASN C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 28676 Z= 0.158 Angle : 0.548 11.828 38903 Z= 0.276 Chirality : 0.043 0.325 4403 Planarity : 0.003 0.045 4911 Dihedral : 4.771 55.263 4093 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 2.42 % Allowed : 14.37 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.42 (0.15), residues: 3489 helix: 1.63 (0.15), residues: 1234 sheet: -0.12 (0.21), residues: 631 loop : -0.57 (0.17), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 609 HIS 0.005 0.001 HIS A 44 PHE 0.055 0.001 PHE D 42 TYR 0.016 0.001 TYR D 330 ARG 0.009 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7991 (m-80) cc_final: 0.7788 (m-80) REVERT: H 116 LEU cc_start: 0.8464 (tp) cc_final: 0.8121 (tt) REVERT: A 324 MET cc_start: 0.8154 (mpp) cc_final: 0.7658 (mpp) REVERT: A 630 MET cc_start: 0.6690 (mtt) cc_final: 0.6457 (mtp) REVERT: A 828 MET cc_start: 0.3610 (tpt) cc_final: 0.2953 (tmm) REVERT: B 58 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8402 (pt) REVERT: B 546 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.4479 (pt) REVERT: B 548 ARG cc_start: 0.3379 (mtm-85) cc_final: 0.1024 (tpt-90) REVERT: B 555 MET cc_start: 0.4065 (OUTLIER) cc_final: 0.3769 (ptm) REVERT: B 607 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4932 (tmm) REVERT: B 639 PHE cc_start: 0.7386 (t80) cc_final: 0.6965 (t80) REVERT: B 702 MET cc_start: 0.7328 (ppp) cc_final: 0.6205 (ppp) REVERT: C 74 MET cc_start: 0.8556 (pmm) cc_final: 0.8109 (pmm) REVERT: C 138 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7657 (mttm) REVERT: C 170 PHE cc_start: 0.8539 (m-10) cc_final: 0.8172 (m-10) REVERT: C 175 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9059 (p) REVERT: C 252 ASP cc_start: 0.8113 (p0) cc_final: 0.7756 (p0) REVERT: C 480 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8943 (p) REVERT: C 653 MET cc_start: 0.6062 (ppp) cc_final: 0.5053 (mmm) REVERT: D 354 MET cc_start: 0.7873 (mmm) cc_final: 0.7507 (mmm) REVERT: D 501 MET cc_start: 0.9250 (ttm) cc_final: 0.8896 (ttm) REVERT: D 607 MET cc_start: 0.5945 (ptt) cc_final: 0.5593 (ppp) REVERT: F 58 VAL cc_start: 0.6149 (t) cc_final: 0.5876 (t) REVERT: G 39 ARG cc_start: 0.7700 (mpp-170) cc_final: 0.6826 (mmt90) REVERT: G 42 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: G 50 MET cc_start: 0.7781 (mmm) cc_final: 0.7330 (mmm) outliers start: 74 outliers final: 42 residues processed: 236 average time/residue: 0.3894 time to fit residues: 149.2560 Evaluate side-chains 215 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 193 optimal weight: 0.1980 chunk 248 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 338 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN E 65 GLN F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 28676 Z= 0.367 Angle : 0.639 12.094 38903 Z= 0.325 Chirality : 0.045 0.404 4403 Planarity : 0.004 0.047 4911 Dihedral : 5.055 46.277 4093 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.10 % Rotamer: Outliers : 2.88 % Allowed : 14.47 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.15 (0.15), residues: 3489 helix: 1.44 (0.15), residues: 1241 sheet: -0.33 (0.21), residues: 628 loop : -0.73 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 609 HIS 0.006 0.001 HIS D 280 PHE 0.059 0.002 PHE D 42 TYR 0.024 0.002 TYR C 180 ARG 0.008 0.001 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 164 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7953 (m-80) cc_final: 0.7719 (m-80) REVERT: H 116 LEU cc_start: 0.8499 (tp) cc_final: 0.8163 (tt) REVERT: A 180 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: A 181 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7379 (mmt-90) REVERT: A 324 MET cc_start: 0.8192 (mpp) cc_final: 0.7649 (mpp) REVERT: A 828 MET cc_start: 0.3713 (tpt) cc_final: 0.3073 (tmm) REVERT: B 58 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8445 (pt) REVERT: B 548 ARG cc_start: 0.3424 (mtm-85) cc_final: 0.0902 (tpt-90) REVERT: B 555 MET cc_start: 0.3942 (OUTLIER) cc_final: 0.3656 (ptm) REVERT: B 607 MET cc_start: 0.5061 (pp-130) cc_final: 0.4814 (tmm) REVERT: B 639 PHE cc_start: 0.7345 (t80) cc_final: 0.6828 (t80) REVERT: B 702 MET cc_start: 0.7469 (ppp) cc_final: 0.6919 (ppp) REVERT: C 74 MET cc_start: 0.8561 (pmm) cc_final: 0.8172 (pmm) REVERT: C 138 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7834 (mttm) REVERT: C 252 ASP cc_start: 0.8233 (p0) cc_final: 0.7826 (p0) REVERT: C 653 MET cc_start: 0.6018 (ppp) cc_final: 0.5087 (mmm) REVERT: D 354 MET cc_start: 0.7924 (mmm) cc_final: 0.7541 (mmm) REVERT: D 501 MET cc_start: 0.9290 (ttm) cc_final: 0.8975 (ttm) REVERT: D 607 MET cc_start: 0.5932 (ptt) cc_final: 0.5546 (ppp) REVERT: F 58 VAL cc_start: 0.6079 (t) cc_final: 0.5743 (t) REVERT: G 39 ARG cc_start: 0.7779 (mpp-170) cc_final: 0.6856 (mmt90) REVERT: G 42 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: G 50 MET cc_start: 0.7864 (mmm) cc_final: 0.7501 (mmm) outliers start: 88 outliers final: 59 residues processed: 235 average time/residue: 0.3896 time to fit residues: 147.7861 Evaluate side-chains 222 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 157 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 555 MET Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN D 393 GLN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN F 37 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28676 Z= 0.169 Angle : 0.557 12.648 38903 Z= 0.280 Chirality : 0.043 0.323 4403 Planarity : 0.003 0.039 4911 Dihedral : 4.725 43.850 4093 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 2.26 % Allowed : 15.58 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.29 (0.15), residues: 3489 helix: 1.55 (0.15), residues: 1237 sheet: -0.21 (0.22), residues: 623 loop : -0.67 (0.17), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 609 HIS 0.006 0.001 HIS A 332 PHE 0.058 0.001 PHE D 42 TYR 0.017 0.001 TYR D 330 ARG 0.007 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 168 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 32 TYR cc_start: 0.7991 (m-80) cc_final: 0.7789 (m-80) REVERT: H 116 LEU cc_start: 0.8454 (tp) cc_final: 0.8100 (tt) REVERT: A 181 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7234 (mmt-90) REVERT: A 324 MET cc_start: 0.8199 (mpp) cc_final: 0.7675 (mpp) REVERT: A 331 MET cc_start: 0.5519 (tmm) cc_final: 0.4994 (tmm) REVERT: A 630 MET cc_start: 0.7000 (mtt) cc_final: 0.6615 (mtp) REVERT: A 828 MET cc_start: 0.3543 (tpt) cc_final: 0.2941 (tmm) REVERT: B 58 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8408 (pt) REVERT: B 502 MET cc_start: 0.8429 (tpt) cc_final: 0.8194 (tpt) REVERT: B 546 ILE cc_start: 0.5566 (OUTLIER) cc_final: 0.4483 (pt) REVERT: B 548 ARG cc_start: 0.3511 (mtm-85) cc_final: 0.0985 (tpt-90) REVERT: B 555 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3797 (ptm) REVERT: B 607 MET cc_start: 0.5210 (OUTLIER) cc_final: 0.4928 (tmm) REVERT: B 639 PHE cc_start: 0.7248 (t80) cc_final: 0.6826 (t80) REVERT: B 702 MET cc_start: 0.7472 (ppp) cc_final: 0.6244 (ppp) REVERT: B 706 MET cc_start: 0.8502 (ppp) cc_final: 0.7948 (ppp) REVERT: C 138 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7720 (mttm) REVERT: C 252 ASP cc_start: 0.8123 (p0) cc_final: 0.7826 (p0) REVERT: C 653 MET cc_start: 0.6065 (ppp) cc_final: 0.5053 (mmm) REVERT: D 354 MET cc_start: 0.7879 (mmm) cc_final: 0.7518 (mmm) REVERT: D 501 MET cc_start: 0.9237 (ttm) cc_final: 0.8869 (ttm) REVERT: D 607 MET cc_start: 0.5905 (ptt) cc_final: 0.5528 (ppp) REVERT: E 3 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 4 MET cc_start: 0.7055 (mmm) cc_final: 0.6521 (mmp) REVERT: G 39 ARG cc_start: 0.7758 (mpp-170) cc_final: 0.6891 (mmt90) REVERT: G 42 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: G 50 MET cc_start: 0.7859 (mmm) cc_final: 0.7414 (mmm) outliers start: 69 outliers final: 46 residues processed: 224 average time/residue: 0.4061 time to fit residues: 147.5927 Evaluate side-chains 214 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 0.0870 chunk 247 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 298 optimal weight: 30.0000 chunk 314 optimal weight: 3.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28676 Z= 0.195 Angle : 0.564 13.479 38903 Z= 0.282 Chirality : 0.043 0.325 4403 Planarity : 0.003 0.040 4911 Dihedral : 4.619 43.988 4093 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 2.23 % Allowed : 15.61 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.29 (0.15), residues: 3489 helix: 1.57 (0.15), residues: 1236 sheet: -0.23 (0.21), residues: 625 loop : -0.68 (0.17), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 609 HIS 0.003 0.001 HIS A 85 PHE 0.057 0.001 PHE D 42 TYR 0.017 0.001 TYR D 330 ARG 0.006 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 163 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 116 LEU cc_start: 0.8455 (tp) cc_final: 0.8099 (tt) REVERT: A 181 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7360 (mmt-90) REVERT: A 324 MET cc_start: 0.8225 (mpp) cc_final: 0.7686 (mpp) REVERT: A 331 MET cc_start: 0.5746 (tmm) cc_final: 0.5408 (tmm) REVERT: A 630 MET cc_start: 0.6894 (mtt) cc_final: 0.6560 (mtp) REVERT: A 828 MET cc_start: 0.3159 (tpt) cc_final: 0.2674 (tmm) REVERT: B 58 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8354 (pt) REVERT: B 502 MET cc_start: 0.8287 (tpt) cc_final: 0.8085 (tpt) REVERT: B 546 ILE cc_start: 0.5609 (OUTLIER) cc_final: 0.4536 (pt) REVERT: B 548 ARG cc_start: 0.3528 (mtm-85) cc_final: 0.0990 (tpt-90) REVERT: B 555 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3824 (ptm) REVERT: B 607 MET cc_start: 0.5053 (OUTLIER) cc_final: 0.4796 (tmm) REVERT: B 639 PHE cc_start: 0.7237 (t80) cc_final: 0.6825 (t80) REVERT: B 702 MET cc_start: 0.7432 (ppp) cc_final: 0.6276 (ppp) REVERT: B 706 MET cc_start: 0.8510 (ppp) cc_final: 0.8216 (ppp) REVERT: C 138 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7743 (mttm) REVERT: C 252 ASP cc_start: 0.8136 (p0) cc_final: 0.7836 (p0) REVERT: C 653 MET cc_start: 0.5983 (ppp) cc_final: 0.5069 (mmm) REVERT: D 354 MET cc_start: 0.7867 (mmm) cc_final: 0.7503 (mmm) REVERT: D 361 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9124 (mt) REVERT: D 501 MET cc_start: 0.9242 (ttm) cc_final: 0.8858 (ttm) REVERT: D 607 MET cc_start: 0.5914 (ptt) cc_final: 0.5527 (ppp) REVERT: E 3 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 4 MET cc_start: 0.7075 (mmm) cc_final: 0.6511 (mmp) REVERT: G 39 ARG cc_start: 0.7904 (mpp-170) cc_final: 0.7040 (mmt90) REVERT: G 42 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: G 50 MET cc_start: 0.7903 (mmm) cc_final: 0.7464 (mmm) outliers start: 68 outliers final: 51 residues processed: 214 average time/residue: 0.3945 time to fit residues: 137.3834 Evaluate side-chains 220 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 203 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 215 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 154 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28676 Z= 0.305 Angle : 0.608 14.570 38903 Z= 0.308 Chirality : 0.044 0.368 4403 Planarity : 0.004 0.040 4911 Dihedral : 4.836 45.143 4093 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 2.52 % Allowed : 15.48 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.15 (0.15), residues: 3489 helix: 1.47 (0.15), residues: 1241 sheet: -0.28 (0.22), residues: 617 loop : -0.80 (0.17), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 609 HIS 0.004 0.001 HIS A 674 PHE 0.058 0.002 PHE D 42 TYR 0.024 0.002 TYR C 180 ARG 0.007 0.000 ARG A 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 165 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7376 (mmt-90) REVERT: A 324 MET cc_start: 0.8257 (mpp) cc_final: 0.7681 (mpp) REVERT: A 331 MET cc_start: 0.5765 (tmm) cc_final: 0.5404 (tmm) REVERT: A 338 MET cc_start: 0.7776 (ptp) cc_final: 0.7572 (ptt) REVERT: A 473 PHE cc_start: 0.4989 (OUTLIER) cc_final: 0.3197 (m-80) REVERT: A 630 MET cc_start: 0.6900 (mtt) cc_final: 0.6590 (mtp) REVERT: A 828 MET cc_start: 0.3076 (tpt) cc_final: 0.2545 (tmm) REVERT: B 58 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8386 (pt) REVERT: B 502 MET cc_start: 0.8324 (tpt) cc_final: 0.8099 (tpt) REVERT: B 555 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3871 (ptm) REVERT: B 607 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4880 (tmm) REVERT: B 639 PHE cc_start: 0.7318 (t80) cc_final: 0.6867 (t80) REVERT: B 702 MET cc_start: 0.7488 (ppp) cc_final: 0.6565 (ppp) REVERT: C 138 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7745 (mttm) REVERT: C 252 ASP cc_start: 0.8219 (p0) cc_final: 0.7884 (p0) REVERT: C 653 MET cc_start: 0.6091 (ppp) cc_final: 0.5157 (mmm) REVERT: C 701 MET cc_start: 0.8443 (ttp) cc_final: 0.8207 (ptm) REVERT: D 354 MET cc_start: 0.7890 (mmm) cc_final: 0.7513 (mmm) REVERT: D 361 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9120 (mt) REVERT: D 501 MET cc_start: 0.9248 (ttm) cc_final: 0.8899 (ttm) REVERT: D 607 MET cc_start: 0.6063 (ptt) cc_final: 0.5817 (ppp) REVERT: E 3 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 4 MET cc_start: 0.7150 (mmm) cc_final: 0.6598 (mmp) REVERT: G 39 ARG cc_start: 0.7940 (mpp-170) cc_final: 0.7017 (mmt90) REVERT: G 42 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: G 50 MET cc_start: 0.7913 (mmm) cc_final: 0.7478 (mmm) outliers start: 77 outliers final: 54 residues processed: 224 average time/residue: 0.4021 time to fit residues: 147.6204 Evaluate side-chains 225 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 163 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain A residue 42 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 355 TYR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 653 MET Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 286 TYR Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 396 PHE Chi-restraints excluded: chain C residue 403 ASP Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 812 ASN Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 HIS ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN D 616 ASN ** D 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.067375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.050848 restraints weight = 156801.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050419 restraints weight = 99457.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.051034 restraints weight = 75627.649| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28676 Z= 0.215 Angle : 0.584 15.114 38903 Z= 0.291 Chirality : 0.043 0.339 4403 Planarity : 0.003 0.040 4911 Dihedral : 4.751 46.171 4093 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 2.39 % Allowed : 15.65 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % 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: 0.17 (0.15), residues: 3489 helix: 1.45 (0.15), residues: 1247 sheet: -0.23 (0.22), residues: 614 loop : -0.78 (0.17), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 609 HIS 0.004 0.001 HIS A 702 PHE 0.057 0.001 PHE D 42 TYR 0.017 0.001 TYR D 330 ARG 0.013 0.000 ARG A 692 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.00 seconds wall clock time: 92 minutes 10.52 seconds (5530.52 seconds total)