Starting phenix.real_space_refine on Fri Mar 15 21:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szf_40914/03_2024/8szf_40914_updated.pdb" } resolution = 2.8 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= 0.013 sd= 0.039 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 72 5.16 5 C 8305 2.51 5 N 2073 2.21 5 O 2351 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12813 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 6243 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 31, 'TRANS': 767} Chain breaks: 3 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 6306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6306 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 31, 'TRANS': 769} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CA': 3, 'PO4': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {' CA': 1, 'NAG': 1, 'PO4': 1, 'SPM': 1, 'YP4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.24, per 1000 atoms: 0.57 Number of scatterers: 12813 At special positions: 0 Unit cell: (103.256, 98.0501, 184.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 72 16.00 P 2 15.00 F 6 9.00 O 2351 8.00 N 2073 7.00 C 8305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.04 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1201 " - " ASN A 261 " " NAG A1202 " - " ASN A 468 " " NAG B1001 " - " ASN B 488 " " NAG B1002 " - " ASN B 468 " " NAG B1007 " - " ASN B 261 " " NAG C 1 " - " ASN A 541 " " NAG D 1 " - " ASN A 488 " " NAG E 1 " - " ASN B 541 " Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 13 sheets defined 43.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 removed outlier: 3.608A pdb=" N MET A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.646A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.720A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.663A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.651A pdb=" N PHE A 311 " --> pdb=" O PRO A 308 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.710A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.580A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.584A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 666 removed outlier: 4.180A pdb=" N LEU A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 666 " --> pdb=" O PHE A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 698 removed outlier: 4.883A pdb=" N GLN A 681 " --> pdb=" O CYS A 677 " (cutoff:3.500A) Proline residue: A 682 - end of helix removed outlier: 3.977A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 removed outlier: 3.682A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 794 removed outlier: 4.037A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 825 removed outlier: 3.852A pdb=" N THR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 809 " --> pdb=" O LYS A 805 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 832 through 861 removed outlier: 4.012A pdb=" N ILE A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.690A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.628A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 118 through 122' Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.792A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.841A pdb=" N GLU B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.577A pdb=" N PHE B 311 " --> pdb=" O PRO B 308 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.912A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 611 through 636 Processing helix chain 'B' and resid 641 through 644 No H-bonds generated for 'chain 'B' and resid 641 through 644' Processing helix chain 'B' and resid 648 through 667 removed outlier: 3.840A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 677 No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 680 through 697 removed outlier: 3.850A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 724 No H-bonds generated for 'chain 'B' and resid 721 through 724' Processing helix chain 'B' and resid 727 through 745 Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.866A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 827 Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 833 through 860 removed outlier: 3.776A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.433A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.386A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.530A pdb=" N GLY A 509 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 550 through 554 Processing sheet with id= E, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= F, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.870A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 749 " --> pdb=" O HIS A 766 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.315A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.473A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.635A pdb=" N GLY B 509 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= K, first strand: chain 'B' and resid 550 through 554 Processing sheet with id= L, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.689A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 764 " --> pdb=" O TYR B 751 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2047 1.31 - 1.44: 3738 1.44 - 1.57: 7254 1.57 - 1.70: 1 1.70 - 1.83: 86 Bond restraints: 13126 Sorted by residual: bond pdb=" CG YP4 A1208 " pdb=" CD1 YP4 A1208 " ideal model delta sigma weight residual 1.426 1.354 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CG YP4 B1006 " pdb=" CD1 YP4 B1006 " ideal model delta sigma weight residual 1.426 1.357 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O3 PO4 B1005 " pdb=" P PO4 B1005 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" O3 PO4 A1207 " pdb=" P PO4 A1207 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" O4 PO4 A1207 " pdb=" P PO4 A1207 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.58e+00 ... (remaining 13121 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.25: 405 107.25 - 113.96: 7285 113.96 - 120.67: 5408 120.67 - 127.37: 4585 127.37 - 134.08: 137 Bond angle restraints: 17820 Sorted by residual: angle pdb=" N PRO B 641 " pdb=" CA PRO B 641 " pdb=" C PRO B 641 " ideal model delta sigma weight residual 113.53 123.39 -9.86 1.39e+00 5.18e-01 5.03e+01 angle pdb=" C CYS A 598 " pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sigma weight residual 109.38 117.80 -8.42 1.80e+00 3.09e-01 2.19e+01 angle pdb=" C PHE A 667 " pdb=" N PHE A 668 " pdb=" CA PHE A 668 " ideal model delta sigma weight residual 121.64 112.56 9.08 2.13e+00 2.20e-01 1.82e+01 angle pdb=" C THR B 640 " pdb=" N PRO B 641 " pdb=" CA PRO B 641 " ideal model delta sigma weight residual 119.05 123.00 -3.95 1.11e+00 8.12e-01 1.27e+01 angle pdb=" CA SER A 597 " pdb=" C SER A 597 " pdb=" O SER A 597 " ideal model delta sigma weight residual 121.06 117.03 4.03 1.16e+00 7.43e-01 1.21e+01 ... (remaining 17815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7140 17.33 - 34.66: 575 34.66 - 51.99: 122 51.99 - 69.32: 17 69.32 - 86.66: 8 Dihedral angle restraints: 7862 sinusoidal: 3206 harmonic: 4656 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 170.80 -77.80 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS A 585 " pdb=" SG CYS A 585 " pdb=" SG CYS A 598 " pdb=" CB CYS A 598 " ideal model delta sinusoidal sigma weight residual 93.00 144.29 -51.29 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C CYS A 598 " pdb=" N CYS A 598 " pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " ideal model delta harmonic sigma weight residual -122.60 -137.04 14.44 0 2.50e+00 1.60e-01 3.34e+01 ... (remaining 7859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1895 0.101 - 0.202: 116 0.202 - 0.303: 5 0.303 - 0.404: 2 0.404 - 0.504: 1 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.00e+00 chirality pdb=" CA CYS A 598 " pdb=" N CYS A 598 " pdb=" C CYS A 598 " pdb=" CB CYS A 598 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CB THR B 640 " pdb=" CA THR B 640 " pdb=" OG1 THR B 640 " pdb=" CG2 THR B 640 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2016 not shown) Planarity restraints: 2247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 578 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C ASP A 578 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP A 578 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 579 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 648 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C ARG A 648 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG A 648 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 649 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 861 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C LEU B 861 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU B 861 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE B 862 " 0.015 2.00e-02 2.50e+03 ... (remaining 2244 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3091 2.79 - 3.32: 11407 3.32 - 3.85: 20035 3.85 - 4.37: 23766 4.37 - 4.90: 41098 Nonbonded interactions: 99397 Sorted by model distance: nonbonded pdb=" OE1 GLU A 456 " pdb=" NE1 TRP A 458 " model vdw 2.268 2.520 nonbonded pdb=" O ALA A 168 " pdb=" N TRP A1203 " model vdw 2.294 2.520 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.314 2.520 nonbonded pdb=" OG1 THR B 470 " pdb=" OE1 GLN B 476 " model vdw 2.316 2.440 nonbonded pdb=" NH1 ARG A 551 " pdb=" O LYS A 552 " model vdw 2.325 2.520 ... (remaining 99392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 119 or (resid 120 through 121 and (name N or na \ me CA or name C or name O or name CB )) or resid 122 through 362 or resid 392 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 635 or (resid 636 and (name N or name CA o \ r name C or name O or name CB )) or resid 637 through 698 or (resid 699 through \ 701 and (name N or name CA or name C or name O or name CB )) or (resid 703 and ( \ name N or name CA or name C or name O or name CB )) or resid 722 through 862 or \ (resid 863 and (name N or name CA or name C or name O or name CB )) or resid 864 \ through 865 or (resid 866 through 867 and (name N or name CA or name C or name \ O or name CB )) or resid 868 through 871 or (resid 872 through 873 and (name N o \ r name CA or name C or name O or name CB )) or resid 874 or resid 1201 through 1 \ 203 or resid 1204)) selection = (chain 'B' and (resid 20 through 123 or (resid 134 through 135 and (name N or na \ me CA or name C or name O or name CB )) or resid 136 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 392 through 404 \ or (resid 405 and (name N or name CA or name C or name O or name CB )) or resid \ 406 through 480 or (resid 481 and (name N or name CA or name C or name O or nam \ e CB )) or resid 482 through 498 or (resid 499 through 500 and (name N or name C \ A or name C or name O or name CB )) or resid 501 through 592 or (resid 593 and ( \ name N or name CA or name C or name O or name CB )) or resid 594 through 601 or \ (resid 602 and (name N or name CA or name C or name O or name CB )) or resid 603 \ through 634 or (resid 635 through 636 and (name N or name CA or name C or name \ O or name CB )) or resid 637 or (resid 638 and (name N or name CA or name C or n \ ame O or name CB )) or resid 639 through 648 or (resid 649 and (name N or name C \ A or name C or name O or name CB )) or resid 650 through 670 or (resid 671 and ( \ name N or name CA or name C or name O or name CB )) or resid 672 through 699 or \ (resid 700 through 701 and (name N or name CA or name C or name O or name CB )) \ or resid 721 through 729 or (resid 730 and (name N or name CA or name C or name \ O or name CB )) or resid 731 through 758 or (resid 759 and (name N or name CA or \ name C or name O or name CB )) or resid 760 through 795 or (resid 796 and (name \ N or name CA or name C or name O or name CB )) or resid 797 through 802 or (res \ id 803 through 804 and (name N or name CA or name C or name O or name CB )) or r \ esid 805 through 853 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 868 or (resid 869 through 873 and (name N or na \ me CA or name C or name O or name CB )) or resid 874 or resid 1001 through 1003 \ or resid 1004)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.970 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.190 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.005 0.095 13126 Z= 0.335 Angle : 0.704 10.025 17820 Z= 0.404 Chirality : 0.052 0.504 2019 Planarity : 0.005 0.047 2239 Dihedral : 13.190 86.655 4796 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1584 helix: 1.35 (0.20), residues: 686 sheet: -0.93 (0.34), residues: 214 loop : -1.01 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 742 HIS 0.006 0.001 HIS A 463 PHE 0.038 0.002 PHE B 789 TYR 0.024 0.002 TYR B 744 ARG 0.006 0.000 ARG B 648 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 536 GLU cc_start: 0.7080 (pp20) cc_final: 0.6860 (pp20) REVERT: B 647 ASN cc_start: 0.6701 (t0) cc_final: 0.6259 (m110) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 1.1304 time to fit residues: 183.6994 Evaluate side-chains 111 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 124 optimal weight: 0.0070 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 49 GLN A 722 ASN B 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13126 Z= 0.161 Angle : 0.512 7.342 17820 Z= 0.276 Chirality : 0.042 0.172 2019 Planarity : 0.004 0.044 2239 Dihedral : 6.111 67.178 1971 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.19 % Allowed : 7.56 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1584 helix: 1.70 (0.19), residues: 689 sheet: -0.91 (0.34), residues: 214 loop : -0.91 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.003 0.001 HIS A 766 PHE 0.014 0.001 PHE B 634 TYR 0.015 0.001 TYR B 858 ARG 0.005 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.493 Fit side-chains REVERT: A 536 GLU cc_start: 0.7071 (pp20) cc_final: 0.6832 (pp20) REVERT: A 793 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7784 (mtpp) REVERT: B 853 PHE cc_start: 0.8240 (m-80) cc_final: 0.8008 (m-80) outliers start: 16 outliers final: 10 residues processed: 128 average time/residue: 1.0977 time to fit residues: 155.9652 Evaluate side-chains 123 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 chunk 143 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 766 HIS B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13126 Z= 0.140 Angle : 0.470 5.250 17820 Z= 0.253 Chirality : 0.041 0.163 2019 Planarity : 0.004 0.044 2239 Dihedral : 5.606 66.217 1971 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.70 % Allowed : 8.90 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1584 helix: 1.82 (0.19), residues: 697 sheet: -0.85 (0.35), residues: 214 loop : -0.81 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.003 0.001 HIS A 429 PHE 0.012 0.001 PHE B 801 TYR 0.012 0.001 TYR B 421 ARG 0.006 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.279 Fit side-chains REVERT: A 285 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7828 (ttp-110) REVERT: A 536 GLU cc_start: 0.7070 (pp20) cc_final: 0.6826 (pp20) REVERT: A 793 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (mtpp) REVERT: B 27 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7959 (pt0) outliers start: 23 outliers final: 8 residues processed: 134 average time/residue: 1.0396 time to fit residues: 154.6230 Evaluate side-chains 122 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 463 HIS A 766 HIS B 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13126 Z= 0.294 Angle : 0.579 6.235 17820 Z= 0.311 Chirality : 0.045 0.168 2019 Planarity : 0.005 0.049 2239 Dihedral : 5.929 65.798 1971 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 10.23 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1584 helix: 1.60 (0.19), residues: 693 sheet: -0.94 (0.34), residues: 220 loop : -0.96 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.020 0.002 PHE A 444 TYR 0.015 0.002 TYR B 421 ARG 0.003 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.323 Fit side-chains REVERT: A 536 GLU cc_start: 0.7159 (pp20) cc_final: 0.6929 (pp20) REVERT: A 793 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7913 (mtpp) REVERT: A 811 MET cc_start: 0.8287 (mmp) cc_final: 0.7901 (mmt) REVERT: B 27 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8099 (pt0) outliers start: 25 outliers final: 13 residues processed: 132 average time/residue: 1.0954 time to fit residues: 160.5412 Evaluate side-chains 126 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 766 HIS B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13126 Z= 0.161 Angle : 0.489 6.609 17820 Z= 0.262 Chirality : 0.042 0.193 2019 Planarity : 0.004 0.052 2239 Dihedral : 5.599 65.114 1971 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.08 % Allowed : 11.34 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1584 helix: 1.70 (0.19), residues: 696 sheet: -0.98 (0.35), residues: 214 loop : -0.87 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 818 HIS 0.002 0.001 HIS B 466 PHE 0.011 0.001 PHE A 444 TYR 0.013 0.001 TYR A 421 ARG 0.014 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.633 Fit side-chains REVERT: A 536 GLU cc_start: 0.7083 (pp20) cc_final: 0.6834 (pp20) REVERT: A 737 VAL cc_start: 0.6984 (OUTLIER) cc_final: 0.6694 (t) REVERT: A 811 MET cc_start: 0.8263 (mmp) cc_final: 0.7907 (mmt) REVERT: B 27 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: B 853 PHE cc_start: 0.8060 (m-80) cc_final: 0.7841 (m-80) outliers start: 28 outliers final: 12 residues processed: 132 average time/residue: 1.1615 time to fit residues: 170.7365 Evaluate side-chains 125 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 766 HIS B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13126 Z= 0.258 Angle : 0.556 6.228 17820 Z= 0.298 Chirality : 0.044 0.166 2019 Planarity : 0.004 0.047 2239 Dihedral : 5.777 64.522 1971 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.52 % Allowed : 11.49 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1584 helix: 1.56 (0.19), residues: 693 sheet: -1.04 (0.34), residues: 222 loop : -0.95 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 818 HIS 0.004 0.001 HIS B 429 PHE 0.018 0.002 PHE A 444 TYR 0.020 0.002 TYR B 435 ARG 0.007 0.001 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.404 Fit side-chains REVERT: A 536 GLU cc_start: 0.7137 (pp20) cc_final: 0.6913 (pp20) REVERT: A 556 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6561 (tp30) REVERT: A 737 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6685 (t) REVERT: B 27 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: B 481 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6396 (pm20) outliers start: 34 outliers final: 17 residues processed: 138 average time/residue: 0.9885 time to fit residues: 152.1129 Evaluate side-chains 134 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.0060 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13126 Z= 0.163 Angle : 0.490 8.770 17820 Z= 0.262 Chirality : 0.042 0.194 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.524 63.748 1971 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 12.16 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1584 helix: 1.69 (0.20), residues: 694 sheet: -1.02 (0.34), residues: 222 loop : -0.87 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 299 HIS 0.002 0.001 HIS B 466 PHE 0.011 0.001 PHE A 444 TYR 0.023 0.001 TYR B 435 ARG 0.007 0.000 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.444 Fit side-chains REVERT: A 285 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7956 (ttp-110) REVERT: A 536 GLU cc_start: 0.7074 (pp20) cc_final: 0.6835 (pp20) REVERT: A 737 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6759 (t) REVERT: A 793 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7841 (ttpp) REVERT: A 811 MET cc_start: 0.8244 (mmp) cc_final: 0.7895 (mmt) REVERT: B 27 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: B 481 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: B 853 PHE cc_start: 0.8056 (m-80) cc_final: 0.7814 (m-80) outliers start: 27 outliers final: 11 residues processed: 129 average time/residue: 1.0226 time to fit residues: 146.9359 Evaluate side-chains 129 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 754 GLN B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13126 Z= 0.218 Angle : 0.531 9.895 17820 Z= 0.284 Chirality : 0.043 0.172 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.621 63.085 1971 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.70 % Allowed : 12.97 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1584 helix: 1.66 (0.19), residues: 690 sheet: -1.03 (0.34), residues: 222 loop : -0.94 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 818 HIS 0.003 0.001 HIS B 429 PHE 0.015 0.001 PHE A 444 TYR 0.022 0.002 TYR B 435 ARG 0.008 0.000 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.275 Fit side-chains REVERT: A 285 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7963 (ttp-110) REVERT: A 536 GLU cc_start: 0.7134 (pp20) cc_final: 0.6904 (pp20) REVERT: A 737 VAL cc_start: 0.7088 (OUTLIER) cc_final: 0.6780 (t) REVERT: A 793 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7785 (ttpp) REVERT: B 27 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: B 270 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: B 481 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6395 (pm20) REVERT: B 853 PHE cc_start: 0.8088 (m-80) cc_final: 0.7825 (m-80) outliers start: 23 outliers final: 13 residues processed: 125 average time/residue: 1.0722 time to fit residues: 149.1041 Evaluate side-chains 127 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 481 GLU Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 151 optimal weight: 0.4980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13126 Z= 0.151 Angle : 0.482 11.263 17820 Z= 0.256 Chirality : 0.041 0.176 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.389 62.261 1971 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.85 % Allowed : 12.82 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1584 helix: 1.71 (0.20), residues: 699 sheet: -1.01 (0.34), residues: 222 loop : -0.83 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 299 HIS 0.002 0.001 HIS A 429 PHE 0.010 0.001 PHE B 469 TYR 0.012 0.001 TYR A 421 ARG 0.007 0.000 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.141 Fit side-chains REVERT: A 285 ARG cc_start: 0.8222 (ttp80) cc_final: 0.7958 (ttp-110) REVERT: A 536 GLU cc_start: 0.7069 (pp20) cc_final: 0.6826 (pp20) REVERT: A 737 VAL cc_start: 0.7035 (OUTLIER) cc_final: 0.6712 (t) REVERT: A 793 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7597 (tmtt) REVERT: B 27 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 270 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: B 853 PHE cc_start: 0.8056 (m-80) cc_final: 0.7777 (m-80) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 1.1559 time to fit residues: 160.1289 Evaluate side-chains 128 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 0.0030 chunk 145 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 134 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN B 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13126 Z= 0.156 Angle : 0.488 13.693 17820 Z= 0.259 Chirality : 0.041 0.180 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.332 61.502 1971 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.48 % Allowed : 13.34 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.21), residues: 1584 helix: 1.72 (0.20), residues: 695 sheet: -0.96 (0.35), residues: 222 loop : -0.83 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 299 HIS 0.002 0.001 HIS B 429 PHE 0.011 0.001 PHE B 853 TYR 0.026 0.001 TYR B 435 ARG 0.008 0.000 ARG B 795 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.208 Fit side-chains REVERT: A 285 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7965 (ttp-110) REVERT: A 536 GLU cc_start: 0.7131 (pp20) cc_final: 0.6845 (pp20) REVERT: A 737 VAL cc_start: 0.7089 (OUTLIER) cc_final: 0.6768 (t) REVERT: A 793 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7561 (tmtt) REVERT: B 27 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: B 270 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: B 853 PHE cc_start: 0.8047 (m-80) cc_final: 0.7717 (m-80) outliers start: 20 outliers final: 13 residues processed: 128 average time/residue: 1.1282 time to fit residues: 159.7840 Evaluate side-chains 125 residues out of total 1394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 793 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 761 ILE Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 820 SER Chi-restraints excluded: chain B residue 868 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A 463 HIS B 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.102343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.082606 restraints weight = 24885.473| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.24 r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13126 Z= 0.173 Angle : 0.503 14.501 17820 Z= 0.267 Chirality : 0.042 0.211 2019 Planarity : 0.004 0.046 2239 Dihedral : 5.368 61.118 1971 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 13.34 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.21), residues: 1584 helix: 1.70 (0.20), residues: 694 sheet: -0.98 (0.34), residues: 222 loop : -0.84 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 818 HIS 0.004 0.001 HIS A 463 PHE 0.012 0.001 PHE A 444 TYR 0.025 0.001 TYR B 435 ARG 0.008 0.000 ARG B 795 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.38 seconds wall clock time: 73 minutes 51.99 seconds (4431.99 seconds total)