Starting phenix.real_space_refine on Wed Mar 20 01:59:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqj_40707/03_2024/8sqj_40707_trim_updated.pdb" } resolution = 3.06 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= 0.015 sd= 1.023 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 86 5.49 5 Mg 1 5.21 5 S 88 5.16 5 C 8242 2.51 5 N 2291 2.21 5 O 2945 1.98 5 H 12389 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26044 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 14700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 14700 Classifications: {'peptide': 929} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2823 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 180} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1138 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2842 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1688 Classifications: {'peptide': 113} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Classifications: {'RNA': 32} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNA': 35} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna3p': 34} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 538 Classifications: {'RNA': 17} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain breaks: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 149 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'RNA': 1, 'undetermined': 3, 'water': 118} Link IDs: {None: 121} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4821 SG CYS A 301 31.699 89.795 112.230 1.00 31.05 S ATOM 4898 SG CYS A 306 32.877 93.103 113.297 1.00 41.25 S ATOM 4963 SG CYS A 310 33.796 89.593 115.174 1.00 30.19 S ATOM 7720 SG CYS A 487 30.320 90.929 90.907 1.00 44.18 S ATOM 10237 SG CYS A 645 30.399 94.305 92.029 1.00 38.26 S ATOM 10247 SG CYS A 646 29.184 91.934 94.440 1.00 49.04 S Time building chain proxies: 12.89, per 1000 atoms: 0.49 Number of scatterers: 26044 At special positions: 0 Unit cell: (93.095, 140.725, 167.787, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 88 16.00 P 86 15.00 Mg 1 11.99 O 2945 8.00 N 2291 7.00 C 8242 6.00 H 12389 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.06 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 306 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 646 " Number of angles added : 6 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 12 sheets defined 44.3% alpha, 11.6% beta 25 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 17.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.887A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.804A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 199 removed outlier: 4.236A pdb=" N LEU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ARG A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 236 through 247 removed outlier: 3.728A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 3.987A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.288A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.548A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.542A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.987A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.512A pdb=" N ASP A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 579 removed outlier: 3.720A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.526A pdb=" N ILE A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.950A pdb=" N GLN A 724 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 725 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 No H-bonds generated for 'chain 'A' and resid 739 through 742' Processing helix chain 'A' and resid 744 through 752 removed outlier: 3.520A pdb=" N HIS A 752 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.511A pdb=" N GLN A 773 " --> pdb=" O THR A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 790 removed outlier: 3.587A pdb=" N TYR A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 857 through 871 removed outlier: 3.609A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.786A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 898 Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 919 through 925 removed outlier: 4.055A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 919 through 925' Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.780A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 76 removed outlier: 3.883A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.866A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.905A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 35 through 81 removed outlier: 3.630A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 98 removed outlier: 3.925A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 33 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.911A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS A 75 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A 113 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.438A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.698A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.092A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.663A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.575A pdb=" N ALA G 43 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN G 33 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL G 41 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 53 through 57 478 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 12.82 Time building geometry restraints manager: 22.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 12356 1.05 - 1.27: 2059 1.27 - 1.48: 6190 1.48 - 1.70: 5613 1.70 - 1.91: 136 Bond restraints: 26354 Sorted by residual: bond pdb=" C4' VSN A1001 " pdb=" O4' VSN A1001 " ideal model delta sigma weight residual 1.282 1.610 -0.328 2.00e-02 2.50e+03 2.70e+02 bond pdb=" O4' VSN A1001 " pdb=" C1' VSN A1001 " ideal model delta sigma weight residual 1.555 1.293 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" C2 VSN A1001 " pdb=" N3 VSN A1001 " ideal model delta sigma weight residual 1.483 1.330 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" C1' VSN A1001 " pdb=" N9 VSN A1001 " ideal model delta sigma weight residual 1.296 1.441 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C5' VSN A1001 " pdb=" C4' VSN A1001 " ideal model delta sigma weight residual 1.516 1.373 0.143 2.00e-02 2.50e+03 5.11e+01 ... (remaining 26349 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.81: 796 106.81 - 113.91: 30617 113.91 - 121.00: 10285 121.00 - 128.09: 5513 128.09 - 135.18: 199 Bond angle restraints: 47410 Sorted by residual: angle pdb=" C1' VSN A1001 " pdb=" N9 VSN A1001 " pdb=" C8 VSN A1001 " ideal model delta sigma weight residual 113.21 127.26 -14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" C1' VSN A1001 " pdb=" N9 VSN A1001 " pdb=" C4 VSN A1001 " ideal model delta sigma weight residual 136.07 124.35 11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" N VAL A 166 " pdb=" CA VAL A 166 " pdb=" C VAL A 166 " ideal model delta sigma weight residual 111.81 109.68 2.13 8.60e-01 1.35e+00 6.12e+00 angle pdb=" O3' U O 2 " pdb=" C3' U O 2 " pdb=" C2' U O 2 " ideal model delta sigma weight residual 109.50 113.21 -3.71 1.50e+00 4.44e-01 6.11e+00 angle pdb=" C3' U O 2 " pdb=" O3' U O 2 " pdb=" P U O 3 " ideal model delta sigma weight residual 120.20 123.69 -3.49 1.50e+00 4.44e-01 5.40e+00 ... (remaining 47405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 12177 35.36 - 70.71: 405 70.71 - 106.07: 28 106.07 - 141.42: 0 141.42 - 176.78: 3 Dihedral angle restraints: 12613 sinusoidal: 7383 harmonic: 5230 Sorted by residual: dihedral pdb=" O4' U O 13 " pdb=" C1' U O 13 " pdb=" N1 U O 13 " pdb=" C2 U O 13 " ideal model delta sinusoidal sigma weight residual 200.00 31.93 168.07 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C O 20 " pdb=" C1' C O 20 " pdb=" N1 C O 20 " pdb=" C2 C O 20 " ideal model delta sinusoidal sigma weight residual 232.00 55.22 176.78 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA THR G 79 " pdb=" C THR G 79 " pdb=" N PRO G 80 " pdb=" CA PRO G 80 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 12610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1780 0.041 - 0.081: 365 0.081 - 0.122: 105 0.122 - 0.163: 7 0.163 - 0.204: 2 Chirality restraints: 2259 Sorted by residual: chirality pdb=" C4' VSN A1001 " pdb=" C5' VSN A1001 " pdb=" O4' VSN A1001 " pdb=" C3' VSN A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' U O 2 " pdb=" C4' U O 2 " pdb=" O3' U O 2 " pdb=" C2' U O 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA ILE A 539 " pdb=" N ILE A 539 " pdb=" C ILE A 539 " pdb=" CB ILE A 539 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2256 not shown) Planarity restraints: 3654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 79 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO G 80 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 112 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 339 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.018 5.00e-02 4.00e+02 ... (remaining 3651 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 72 1.91 - 2.58: 24583 2.58 - 3.26: 75333 3.26 - 3.93: 96233 3.93 - 4.60: 152421 Nonbonded interactions: 348642 Sorted by model distance: nonbonded pdb=" H2 ASN G 1 " pdb=" P A O 1 " model vdw 1.239 2.850 nonbonded pdb=" H1 ASN G 1 " pdb=" P A O 1 " model vdw 1.379 2.850 nonbonded pdb="HD21 ASN B 43 " pdb=" H5' G T 122 " model vdw 1.465 2.270 nonbonded pdb=" O4 U P 15 " pdb=" H61 A T 123 " model vdw 1.586 1.850 nonbonded pdb=" N ASN G 1 " pdb=" P A O 1 " model vdw 1.600 3.350 ... (remaining 348637 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 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or (resid 8 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 9 \ through 22 or (resid 23 through 24 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 7 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 27 through 31 or (resid 3 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 34 or (resid 35 through 36 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 37 through 53 or (resid 54 \ and (name N or name CA or name C or name O or name CB or name HA or name HB1 or \ name HB2 or name HB3)) or resid 55 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ or \ name NH1 or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or na \ me HH22)) or resid 76 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.410 Extract box with map and model: 5.160 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 112.850 Find NCS groups from input model: 0.630 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:3.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 13965 Z= 0.364 Angle : 0.512 14.052 19341 Z= 0.270 Chirality : 0.038 0.204 2259 Planarity : 0.003 0.039 2162 Dihedral : 16.183 176.781 5625 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.69 % Allowed : 5.11 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.63 (0.22), residues: 1476 helix: 0.54 (0.21), residues: 675 sheet: 0.07 (0.38), residues: 175 loop : -1.64 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.012 0.002 PHE D 92 TYR 0.010 0.001 TYR A 80 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 227 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7263 (ttt180) REVERT: A 116 ARG cc_start: 0.8199 (mpp-170) cc_final: 0.7346 (mtt90) REVERT: A 189 THR cc_start: 0.8988 (t) cc_final: 0.8757 (m) REVERT: A 284 ASP cc_start: 0.8391 (t70) cc_final: 0.8159 (m-30) REVERT: A 360 ASN cc_start: 0.7896 (t0) cc_final: 0.7376 (p0) REVERT: A 555 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7061 (mtm180) REVERT: A 668 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8298 (tmm) REVERT: A 749 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8572 (mp) REVERT: A 790 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.9007 (t0) REVERT: A 899 MET cc_start: 0.8355 (ttp) cc_final: 0.8077 (ttm) REVERT: A 909 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5823 (m-40) REVERT: B 62 MET cc_start: 0.6973 (mmm) cc_final: 0.6433 (tpt) REVERT: B 70 MET cc_start: 0.7334 (ttm) cc_final: 0.7034 (tmm) REVERT: B 71 TYR cc_start: 0.6916 (t80) cc_final: 0.6474 (t80) REVERT: B 87 MET cc_start: 0.8869 (mtm) cc_final: 0.8654 (mtp) REVERT: B 139 LYS cc_start: 0.8446 (ttpt) cc_final: 0.8112 (ttpp) REVERT: B 174 MET cc_start: 0.8292 (tpt) cc_final: 0.7999 (tpp) REVERT: D 50 ASP cc_start: 0.7375 (t0) cc_final: 0.7105 (m-30) REVERT: D 62 MET cc_start: 0.6608 (mtp) cc_final: 0.6302 (mmt) REVERT: D 96 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8092 (ttm-80) REVERT: D 136 ASN cc_start: 0.6584 (m-40) cc_final: 0.6289 (t0) REVERT: D 168 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7528 (mp10) REVERT: G 19 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7721 (m) REVERT: G 81 LYS cc_start: 0.4409 (OUTLIER) cc_final: 0.3540 (mmmt) outliers start: 47 outliers final: 15 residues processed: 263 average time/residue: 0.6795 time to fit residues: 245.3845 Evaluate side-chains 189 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13965 Z= 0.311 Angle : 0.530 6.510 19341 Z= 0.282 Chirality : 0.039 0.188 2259 Planarity : 0.004 0.037 2162 Dihedral : 17.108 177.371 2957 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.30 % Allowed : 8.41 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.22), residues: 1476 helix: 0.82 (0.21), residues: 675 sheet: -0.01 (0.37), residues: 177 loop : -1.64 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.011 0.001 HIS C 36 PHE 0.015 0.002 PHE D 92 TYR 0.014 0.002 TYR A 719 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7248 (ttt180) REVERT: A 116 ARG cc_start: 0.8205 (mpp-170) cc_final: 0.7360 (mtt90) REVERT: A 189 THR cc_start: 0.9043 (t) cc_final: 0.8771 (m) REVERT: A 284 ASP cc_start: 0.8402 (t70) cc_final: 0.8201 (m-30) REVERT: A 555 ARG cc_start: 0.7540 (mtp85) cc_final: 0.7051 (mtm180) REVERT: A 668 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8296 (tmm) REVERT: A 749 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 62 MET cc_start: 0.6845 (mmm) cc_final: 0.6361 (tpt) REVERT: B 70 MET cc_start: 0.7503 (ttm) cc_final: 0.7043 (tmm) REVERT: B 75 ARG cc_start: 0.7448 (tpt170) cc_final: 0.7004 (tmm160) REVERT: B 87 MET cc_start: 0.8920 (mtm) cc_final: 0.8689 (mtp) REVERT: B 174 MET cc_start: 0.8321 (tpt) cc_final: 0.8014 (tpp) REVERT: D 50 ASP cc_start: 0.7526 (t0) cc_final: 0.7259 (m-30) REVERT: D 62 MET cc_start: 0.6679 (mtp) cc_final: 0.6242 (mmt) REVERT: D 96 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8061 (ttm-80) REVERT: D 168 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7472 (mp10) REVERT: G 19 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7822 (m) REVERT: G 81 LYS cc_start: 0.4407 (OUTLIER) cc_final: 0.3510 (mmmt) outliers start: 42 outliers final: 28 residues processed: 189 average time/residue: 0.6541 time to fit residues: 171.3244 Evaluate side-chains 186 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13965 Z= 0.228 Angle : 0.484 6.306 19341 Z= 0.255 Chirality : 0.037 0.174 2259 Planarity : 0.003 0.038 2162 Dihedral : 16.928 177.313 2955 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.46 % Allowed : 8.72 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1476 helix: 1.15 (0.21), residues: 671 sheet: -0.07 (0.37), residues: 178 loop : -1.59 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.012 0.001 PHE D 92 TYR 0.011 0.001 TYR A 831 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7284 (ttt180) REVERT: A 110 MET cc_start: 0.8147 (mmm) cc_final: 0.7850 (mtm) REVERT: A 116 ARG cc_start: 0.8168 (mpp-170) cc_final: 0.7348 (mtt90) REVERT: A 189 THR cc_start: 0.9070 (t) cc_final: 0.8793 (m) REVERT: A 284 ASP cc_start: 0.8386 (t70) cc_final: 0.8169 (m-30) REVERT: A 555 ARG cc_start: 0.7494 (mtp85) cc_final: 0.6964 (mtm180) REVERT: A 608 ASP cc_start: 0.8050 (t0) cc_final: 0.7776 (t0) REVERT: A 668 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8322 (tmm) REVERT: A 749 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8619 (mp) REVERT: B 62 MET cc_start: 0.6844 (mmm) cc_final: 0.6300 (tpt) REVERT: B 70 MET cc_start: 0.7628 (ttm) cc_final: 0.7058 (tmm) REVERT: B 71 TYR cc_start: 0.6789 (t80) cc_final: 0.6461 (t80) REVERT: B 75 ARG cc_start: 0.7400 (tpt170) cc_final: 0.6948 (tmm160) REVERT: B 87 MET cc_start: 0.8914 (mtm) cc_final: 0.8685 (mtp) REVERT: B 174 MET cc_start: 0.8281 (tpt) cc_final: 0.7977 (tpp) REVERT: C 21 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7515 (mtt-85) REVERT: D 50 ASP cc_start: 0.7552 (t0) cc_final: 0.7249 (m-30) REVERT: D 55 MET cc_start: 0.8071 (tpt) cc_final: 0.7764 (tpp) REVERT: D 59 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7225 (tt) REVERT: D 62 MET cc_start: 0.6659 (mtp) cc_final: 0.6412 (mmt) REVERT: D 87 MET cc_start: 0.8810 (tpt) cc_final: 0.8448 (mmt) REVERT: D 168 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7416 (mp10) REVERT: G 19 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7767 (m) REVERT: G 81 LYS cc_start: 0.4290 (OUTLIER) cc_final: 0.3474 (mmmt) outliers start: 44 outliers final: 32 residues processed: 192 average time/residue: 0.6383 time to fit residues: 172.7370 Evaluate side-chains 196 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13965 Z= 0.255 Angle : 0.493 6.152 19341 Z= 0.260 Chirality : 0.037 0.169 2259 Planarity : 0.004 0.049 2162 Dihedral : 16.804 177.359 2949 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.69 % Allowed : 8.96 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.11 (0.22), residues: 1476 helix: 1.27 (0.21), residues: 672 sheet: -0.07 (0.37), residues: 176 loop : -1.60 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.013 0.001 PHE D 92 TYR 0.012 0.001 TYR A 831 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7312 (ttt180) REVERT: A 110 MET cc_start: 0.8171 (mmm) cc_final: 0.7938 (mtm) REVERT: A 116 ARG cc_start: 0.8257 (mpp-170) cc_final: 0.7387 (mtt90) REVERT: A 189 THR cc_start: 0.9074 (t) cc_final: 0.8768 (m) REVERT: A 284 ASP cc_start: 0.8424 (t70) cc_final: 0.8173 (m-30) REVERT: A 555 ARG cc_start: 0.7506 (mtp85) cc_final: 0.6858 (mtm180) REVERT: A 608 ASP cc_start: 0.8047 (t0) cc_final: 0.7599 (t0) REVERT: A 615 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9082 (ptp) REVERT: A 668 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8328 (tmm) REVERT: A 749 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 899 MET cc_start: 0.8502 (ttp) cc_final: 0.8294 (ttt) REVERT: B 70 MET cc_start: 0.7631 (ttm) cc_final: 0.7091 (tmm) REVERT: B 71 TYR cc_start: 0.6735 (t80) cc_final: 0.6415 (t80) REVERT: B 75 ARG cc_start: 0.7371 (tpt170) cc_final: 0.6934 (tmm160) REVERT: B 87 MET cc_start: 0.8932 (mtm) cc_final: 0.8680 (mtp) REVERT: B 174 MET cc_start: 0.8294 (tpt) cc_final: 0.7984 (tpp) REVERT: D 50 ASP cc_start: 0.7525 (t0) cc_final: 0.7196 (m-30) REVERT: D 55 MET cc_start: 0.8052 (tpt) cc_final: 0.7749 (tpp) REVERT: D 59 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7222 (tt) REVERT: D 62 MET cc_start: 0.6639 (mtp) cc_final: 0.6411 (mmt) REVERT: D 87 MET cc_start: 0.8825 (tpt) cc_final: 0.8482 (mmt) REVERT: D 168 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7314 (mp10) REVERT: G 19 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7800 (m) REVERT: G 81 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3488 (mmmt) outliers start: 47 outliers final: 35 residues processed: 192 average time/residue: 0.6425 time to fit residues: 173.6441 Evaluate side-chains 199 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13965 Z= 0.228 Angle : 0.478 6.169 19341 Z= 0.252 Chirality : 0.037 0.166 2259 Planarity : 0.003 0.038 2162 Dihedral : 16.728 177.454 2949 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.14 % Allowed : 9.90 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.01 (0.22), residues: 1476 helix: 1.35 (0.21), residues: 679 sheet: -0.05 (0.37), residues: 178 loop : -1.58 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.013 0.001 PHE D 92 TYR 0.012 0.001 TYR A 831 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 164 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7932 (ttm170) cc_final: 0.7298 (ttt180) REVERT: A 116 ARG cc_start: 0.8243 (mpp-170) cc_final: 0.7379 (mtt90) REVERT: A 189 THR cc_start: 0.9074 (t) cc_final: 0.8765 (m) REVERT: A 270 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8643 (mp) REVERT: A 284 ASP cc_start: 0.8423 (t70) cc_final: 0.8202 (m-30) REVERT: A 555 ARG cc_start: 0.7529 (mtp85) cc_final: 0.6858 (mtm180) REVERT: A 608 ASP cc_start: 0.8091 (t0) cc_final: 0.7661 (t0) REVERT: A 615 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9087 (ptp) REVERT: A 668 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8344 (tmm) REVERT: A 723 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8465 (tt) REVERT: A 749 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 62 MET cc_start: 0.6498 (mmm) cc_final: 0.6218 (tpt) REVERT: B 70 MET cc_start: 0.7642 (ttm) cc_final: 0.7166 (tmm) REVERT: B 71 TYR cc_start: 0.6664 (t80) cc_final: 0.6380 (t80) REVERT: B 75 ARG cc_start: 0.7396 (tpt170) cc_final: 0.6902 (tmm160) REVERT: B 87 MET cc_start: 0.8871 (mtm) cc_final: 0.8663 (mtp) REVERT: B 174 MET cc_start: 0.8268 (tpt) cc_final: 0.7971 (tpp) REVERT: D 50 ASP cc_start: 0.7526 (t0) cc_final: 0.7176 (m-30) REVERT: D 55 MET cc_start: 0.8061 (tpt) cc_final: 0.7765 (tpp) REVERT: D 59 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7218 (tt) REVERT: D 62 MET cc_start: 0.6630 (mtp) cc_final: 0.6404 (mmt) REVERT: D 87 MET cc_start: 0.8818 (tpt) cc_final: 0.8474 (mmt) REVERT: D 168 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7306 (mp10) REVERT: G 81 LYS cc_start: 0.4334 (OUTLIER) cc_final: 0.3542 (mmmt) outliers start: 40 outliers final: 32 residues processed: 191 average time/residue: 0.6441 time to fit residues: 173.3436 Evaluate side-chains 198 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13965 Z= 0.235 Angle : 0.481 6.125 19341 Z= 0.253 Chirality : 0.037 0.165 2259 Planarity : 0.003 0.036 2162 Dihedral : 16.633 177.556 2946 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.93 % Allowed : 9.51 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1476 helix: 1.40 (0.21), residues: 679 sheet: 0.00 (0.37), residues: 176 loop : -1.60 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.013 0.001 PHE D 92 TYR 0.012 0.001 TYR A 831 ARG 0.002 0.000 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7285 (ttt180) REVERT: A 116 ARG cc_start: 0.8250 (mpp-170) cc_final: 0.7367 (mtt90) REVERT: A 189 THR cc_start: 0.9079 (t) cc_final: 0.8763 (m) REVERT: A 270 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8642 (mp) REVERT: A 284 ASP cc_start: 0.8409 (t70) cc_final: 0.8153 (m-30) REVERT: A 372 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8384 (tt) REVERT: A 555 ARG cc_start: 0.7467 (mtp85) cc_final: 0.6876 (mtm180) REVERT: A 608 ASP cc_start: 0.8063 (t0) cc_final: 0.7628 (t0) REVERT: A 615 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9112 (ptp) REVERT: A 668 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8344 (tmm) REVERT: A 723 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8475 (tt) REVERT: A 731 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8926 (mp) REVERT: A 749 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 62 MET cc_start: 0.6418 (mmm) cc_final: 0.6108 (tpt) REVERT: B 70 MET cc_start: 0.7676 (ttm) cc_final: 0.7204 (tmm) REVERT: B 71 TYR cc_start: 0.6649 (t80) cc_final: 0.6390 (t80) REVERT: B 75 ARG cc_start: 0.7328 (tpt170) cc_final: 0.6821 (tmm160) REVERT: B 87 MET cc_start: 0.8874 (mtm) cc_final: 0.8655 (mtp) REVERT: B 174 MET cc_start: 0.8270 (tpt) cc_final: 0.7972 (tpp) REVERT: D 50 ASP cc_start: 0.7485 (t0) cc_final: 0.7139 (m-30) REVERT: D 55 MET cc_start: 0.8070 (tpt) cc_final: 0.7788 (tpp) REVERT: D 59 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7223 (tt) REVERT: D 62 MET cc_start: 0.6618 (mtp) cc_final: 0.6404 (mmt) REVERT: D 87 MET cc_start: 0.8827 (tpt) cc_final: 0.8474 (mmt) REVERT: D 168 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7264 (mp10) REVERT: G 81 LYS cc_start: 0.4211 (OUTLIER) cc_final: 0.3539 (mmmt) outliers start: 50 outliers final: 36 residues processed: 197 average time/residue: 0.6217 time to fit residues: 172.7157 Evaluate side-chains 205 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13965 Z= 0.178 Angle : 0.459 6.381 19341 Z= 0.241 Chirality : 0.036 0.161 2259 Planarity : 0.003 0.041 2162 Dihedral : 16.572 177.593 2946 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.46 % Allowed : 10.76 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.21 (0.22), residues: 1476 helix: 1.55 (0.22), residues: 681 sheet: 0.09 (0.37), residues: 178 loop : -1.50 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.012 0.001 PHE D 92 TYR 0.011 0.001 TYR A 831 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7894 (ttm170) cc_final: 0.7262 (ttt180) REVERT: A 116 ARG cc_start: 0.8204 (mpp-170) cc_final: 0.7328 (mtt90) REVERT: A 189 THR cc_start: 0.9060 (t) cc_final: 0.8754 (m) REVERT: A 270 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8637 (mp) REVERT: A 284 ASP cc_start: 0.8379 (t70) cc_final: 0.8144 (m-30) REVERT: A 555 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6942 (mtm180) REVERT: A 608 ASP cc_start: 0.8087 (t0) cc_final: 0.7655 (t0) REVERT: A 615 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.9130 (ptp) REVERT: A 668 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8349 (tmm) REVERT: A 731 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8944 (mp) REVERT: A 749 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8620 (mp) REVERT: B 62 MET cc_start: 0.6351 (mmm) cc_final: 0.6040 (tpt) REVERT: B 70 MET cc_start: 0.7660 (ttm) cc_final: 0.7177 (tmm) REVERT: B 75 ARG cc_start: 0.7284 (tpt170) cc_final: 0.6763 (tmm160) REVERT: B 87 MET cc_start: 0.8896 (mtm) cc_final: 0.8657 (mtp) REVERT: B 174 MET cc_start: 0.8256 (tpt) cc_final: 0.7963 (tpp) REVERT: D 55 MET cc_start: 0.8055 (tpt) cc_final: 0.7781 (tpp) REVERT: D 59 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7183 (tt) REVERT: D 62 MET cc_start: 0.6608 (mtp) cc_final: 0.6399 (mmt) REVERT: D 87 MET cc_start: 0.8812 (tpt) cc_final: 0.8457 (mmt) REVERT: D 168 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7251 (mp10) REVERT: G 81 LYS cc_start: 0.4101 (OUTLIER) cc_final: 0.3459 (mmmt) outliers start: 44 outliers final: 32 residues processed: 192 average time/residue: 0.6568 time to fit residues: 176.2636 Evaluate side-chains 197 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13965 Z= 0.242 Angle : 0.478 6.229 19341 Z= 0.252 Chirality : 0.037 0.164 2259 Planarity : 0.003 0.040 2162 Dihedral : 16.576 177.569 2946 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.06 % Allowed : 10.92 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1476 helix: 1.49 (0.21), residues: 683 sheet: 0.09 (0.37), residues: 176 loop : -1.50 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.008 0.001 HIS C 36 PHE 0.013 0.001 PHE D 92 TYR 0.012 0.001 TYR A 831 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7920 (ttm170) cc_final: 0.7275 (ttt180) REVERT: A 116 ARG cc_start: 0.8250 (mpp-170) cc_final: 0.7364 (mtt90) REVERT: A 189 THR cc_start: 0.9069 (t) cc_final: 0.8752 (m) REVERT: A 270 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 284 ASP cc_start: 0.8385 (t70) cc_final: 0.8156 (m-30) REVERT: A 372 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8391 (tt) REVERT: A 555 ARG cc_start: 0.7479 (mtp85) cc_final: 0.6935 (mtm180) REVERT: A 608 ASP cc_start: 0.8183 (t0) cc_final: 0.7740 (t0) REVERT: A 615 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9126 (ptp) REVERT: A 668 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: A 749 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8626 (mp) REVERT: B 70 MET cc_start: 0.7644 (ttm) cc_final: 0.7184 (tmm) REVERT: B 75 ARG cc_start: 0.7315 (tpt170) cc_final: 0.6806 (tmm160) REVERT: B 87 MET cc_start: 0.8873 (mtm) cc_final: 0.8657 (mtp) REVERT: B 174 MET cc_start: 0.8269 (tpt) cc_final: 0.7971 (tpp) REVERT: D 59 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7193 (tt) REVERT: D 87 MET cc_start: 0.8824 (tpt) cc_final: 0.8477 (mmt) REVERT: D 168 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7262 (mp10) REVERT: G 81 LYS cc_start: 0.4180 (OUTLIER) cc_final: 0.3546 (mmmt) outliers start: 39 outliers final: 32 residues processed: 187 average time/residue: 0.6542 time to fit residues: 171.2290 Evaluate side-chains 198 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13965 Z= 0.163 Angle : 0.451 6.167 19341 Z= 0.236 Chirality : 0.036 0.158 2259 Planarity : 0.003 0.039 2162 Dihedral : 16.528 177.565 2945 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.99 % Allowed : 11.08 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.35 (0.23), residues: 1476 helix: 1.64 (0.22), residues: 685 sheet: 0.09 (0.37), residues: 180 loop : -1.40 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.011 0.001 PHE D 92 TYR 0.010 0.001 TYR A 831 ARG 0.002 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.126 Fit side-chains REVERT: A 74 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7255 (ttt180) REVERT: A 189 THR cc_start: 0.9067 (t) cc_final: 0.8752 (m) REVERT: A 270 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8635 (mp) REVERT: A 284 ASP cc_start: 0.8375 (t70) cc_final: 0.8125 (m-30) REVERT: A 372 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 555 ARG cc_start: 0.7490 (mtp85) cc_final: 0.6941 (mtm180) REVERT: A 608 ASP cc_start: 0.8171 (t0) cc_final: 0.7736 (t0) REVERT: A 615 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9115 (ptp) REVERT: A 668 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8355 (tmm) REVERT: A 731 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8955 (mp) REVERT: A 749 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 70 MET cc_start: 0.7598 (ttm) cc_final: 0.7158 (tmm) REVERT: B 75 ARG cc_start: 0.7267 (tpt170) cc_final: 0.6749 (tmm160) REVERT: B 87 MET cc_start: 0.8889 (mtm) cc_final: 0.8654 (mtp) REVERT: B 174 MET cc_start: 0.8250 (tpt) cc_final: 0.7959 (tpp) REVERT: D 59 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7169 (tt) REVERT: D 87 MET cc_start: 0.8804 (tpt) cc_final: 0.8460 (mmt) REVERT: D 97 LYS cc_start: 0.7788 (tttt) cc_final: 0.7373 (ttpt) REVERT: D 168 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7262 (mp10) REVERT: G 81 LYS cc_start: 0.4298 (OUTLIER) cc_final: 0.3664 (mmmt) outliers start: 38 outliers final: 29 residues processed: 182 average time/residue: 0.6856 time to fit residues: 173.5349 Evaluate side-chains 193 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 30.0000 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13965 Z= 0.380 Angle : 0.536 6.366 19341 Z= 0.284 Chirality : 0.040 0.168 2259 Planarity : 0.004 0.040 2162 Dihedral : 16.626 177.428 2942 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.99 % Allowed : 11.15 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.01 (0.22), residues: 1476 helix: 1.32 (0.21), residues: 677 sheet: 0.04 (0.37), residues: 177 loop : -1.52 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.011 0.002 HIS C 36 PHE 0.016 0.002 PHE A 440 TYR 0.014 0.002 TYR A 831 ARG 0.003 0.000 ARG A 721 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.949 Fit side-chains REVERT: A 74 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7293 (ttt180) REVERT: A 116 ARG cc_start: 0.8299 (mpp-170) cc_final: 0.7371 (mtt90) REVERT: A 189 THR cc_start: 0.9091 (t) cc_final: 0.8746 (m) REVERT: A 270 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 284 ASP cc_start: 0.8419 (t70) cc_final: 0.8154 (m-30) REVERT: A 372 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 555 ARG cc_start: 0.7471 (mtp85) cc_final: 0.6895 (mtm180) REVERT: A 608 ASP cc_start: 0.8253 (t0) cc_final: 0.7860 (t0) REVERT: A 615 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9161 (ptp) REVERT: A 668 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8402 (tmm) REVERT: A 731 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8945 (mp) REVERT: A 749 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8611 (mp) REVERT: B 70 MET cc_start: 0.7637 (ttm) cc_final: 0.7064 (ppp) REVERT: B 75 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6857 (tmm160) REVERT: B 77 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7594 (tm-30) REVERT: B 87 MET cc_start: 0.8916 (mtm) cc_final: 0.8682 (mtp) REVERT: B 174 MET cc_start: 0.8276 (tpt) cc_final: 0.8073 (tpp) REVERT: D 59 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7214 (tt) REVERT: D 87 MET cc_start: 0.8849 (tpt) cc_final: 0.8515 (mmt) REVERT: D 157 GLN cc_start: 0.6847 (mm110) cc_final: 0.6519 (mm110) REVERT: D 168 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7268 (mp10) REVERT: G 81 LYS cc_start: 0.4337 (OUTLIER) cc_final: 0.3678 (mmmt) outliers start: 38 outliers final: 29 residues processed: 188 average time/residue: 0.6428 time to fit residues: 167.5976 Evaluate side-chains 197 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104720 restraints weight = 37815.396| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.44 r_work: 0.2776 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13965 Z= 0.126 Angle : 0.448 6.610 19341 Z= 0.234 Chirality : 0.036 0.155 2259 Planarity : 0.003 0.037 2162 Dihedral : 16.541 177.573 2942 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.75 % Allowed : 11.55 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.36 (0.23), residues: 1476 helix: 1.63 (0.22), residues: 686 sheet: 0.10 (0.37), residues: 180 loop : -1.38 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.003 0.001 HIS C 36 PHE 0.009 0.001 PHE A 753 TYR 0.009 0.001 TYR A 831 ARG 0.001 0.000 ARG A 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6275.76 seconds wall clock time: 111 minutes 13.75 seconds (6673.75 seconds total)