Starting phenix.real_space_refine on Mon Jul 22 19:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tyo_41727/07_2024/8tyo_41727.cif" } resolution = 2.75 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= 0.001 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 12401 2.51 5 N 3198 2.21 5 O 3781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19458 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6104 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 749} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5824 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 717} Chain breaks: 11 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7124 Classifications: {'peptide': 913} Link IDs: {'PTRANS': 42, 'TRANS': 870} Chain breaks: 10 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 10.34, per 1000 atoms: 0.53 Number of scatterers: 19458 At special positions: 0 Unit cell: (132.24, 129.92, 162.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3781 8.00 N 3198 7.00 C 12401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C1098 " " NAG D 1 " - " ASN C 717 " Time building additional restraints: 7.46 Conformation dependent library (CDL) restraints added in 3.3 seconds 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 28.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.724A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.581A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.734A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.537A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 991 through 1032 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.562A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.123A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.883A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.093A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.827A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.991A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.134A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.504A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.106A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.557A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.838A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.816A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.631A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.932A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.638A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.664A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.865A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.757A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.394A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.005A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.864A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.555A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.841A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.806A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.065A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.375A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.556A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.677A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.964A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.596A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.551A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.019A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 1094 through 1097 864 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6204 1.35 - 1.47: 4911 1.47 - 1.59: 8630 1.59 - 1.71: 0 1.71 - 1.84: 102 Bond restraints: 19847 Sorted by residual: bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.43e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 ... (remaining 19842 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.94: 398 105.94 - 112.95: 10973 112.95 - 119.96: 6346 119.96 - 126.98: 9117 126.98 - 133.99: 151 Bond angle restraints: 26985 Sorted by residual: angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" CA PRO C 225 " pdb=" N PRO C 225 " pdb=" CD PRO C 225 " ideal model delta sigma weight residual 112.00 108.22 3.78 1.40e+00 5.10e-01 7.29e+00 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 113.93 -3.23 1.22e+00 6.72e-01 7.00e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 113.85 -3.15 1.22e+00 6.72e-01 6.67e+00 angle pdb=" N GLY B 283 " pdb=" CA GLY B 283 " pdb=" C GLY B 283 " ideal model delta sigma weight residual 113.18 119.19 -6.01 2.37e+00 1.78e-01 6.44e+00 ... (remaining 26980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 11380 21.28 - 42.56: 681 42.56 - 63.84: 104 63.84 - 85.12: 25 85.12 - 106.40: 13 Dihedral angle restraints: 12203 sinusoidal: 5099 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.26 84.26 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -144.48 58.48 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 -37.66 -48.34 1 1.00e+01 1.00e-02 3.22e+01 ... (remaining 12200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2415 0.044 - 0.088: 533 0.088 - 0.132: 265 0.132 - 0.176: 10 0.176 - 0.220: 2 Chirality restraints: 3225 Sorted by residual: chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 3222 not shown) Planarity restraints: 3452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO C 225 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " 0.055 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 621 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.015 2.00e-02 2.50e+03 1.47e-02 3.80e+00 pdb=" CG PHE A 906 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.002 2.00e-02 2.50e+03 ... (remaining 3449 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 218 2.66 - 3.22: 17237 3.22 - 3.78: 28483 3.78 - 4.34: 40424 4.34 - 4.90: 68577 Nonbonded interactions: 154939 Sorted by model distance: nonbonded pdb=" OG SER C 605 " pdb=" OE1 GLN C 607 " model vdw 2.100 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.190 2.440 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.237 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.241 2.440 ... (remaining 154934 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 27 through 65 or resid 88 through 107 or resid 116 through \ 122 or resid 124 through 130 or resid 168 through 172 or resid 189 through 196 \ or (resid 197 and (name N or name CA or name C or name O or name CB )) or resid \ 198 through 330 or resid 531 through 620 or resid 641 through 676 or resid 690 t \ hrough 1140 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 130 or resid 168 through 676 or resid 690 throu \ gh 1140 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 65 or resid 88 through 95 or (resid 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 through 107 or resi \ d 116 through 122 or resid 124 through 196 or (resid 197 and (name N or name CA \ or name C or name O or name CB )) or resid 198 through 330 or resid 531 through \ 811 or resid 813 through 1140 or resid 1301 through 1309)) } 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.790 Find NCS groups from input model: 1.300 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: 0.010 Load rotamer database and sin/cos tables:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19847 Z= 0.227 Angle : 0.515 7.540 26985 Z= 0.265 Chirality : 0.044 0.220 3225 Planarity : 0.004 0.117 3425 Dihedral : 13.935 106.400 7532 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.72 (0.17), residues: 2383 helix: 2.60 (0.21), residues: 593 sheet: 0.84 (0.21), residues: 550 loop : -0.79 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.034 0.001 PHE A 906 TYR 0.017 0.001 TYR C 369 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 2.171 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7550 (m-30) cc_final: 0.7325 (m-30) REVERT: A 544 ASN cc_start: 0.7342 (m110) cc_final: 0.7010 (m-40) REVERT: A 856 ASN cc_start: 0.7485 (m110) cc_final: 0.7117 (m110) REVERT: A 902 MET cc_start: 0.8502 (mmp) cc_final: 0.8054 (mmt) REVERT: A 1138 TYR cc_start: 0.7073 (m-80) cc_final: 0.6805 (m-80) REVERT: B 282 ASN cc_start: 0.6525 (m-40) cc_final: 0.5542 (t0) REVERT: B 558 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7328 (mmmm) REVERT: B 1010 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7194 (pt0) REVERT: C 658 ASN cc_start: 0.7195 (m110) cc_final: 0.6950 (m-40) REVERT: C 773 GLU cc_start: 0.7656 (tt0) cc_final: 0.7442 (tt0) REVERT: C 921 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7670 (mttp) REVERT: C 1050 MET cc_start: 0.8356 (ptp) cc_final: 0.8152 (ptm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 1.1786 time to fit residues: 306.0728 Evaluate side-chains 163 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 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 52 GLN A 901 GLN A 955 ASN A 969 ASN A1101 HIS B 901 GLN B 969 ASN C 87 ASN C 564 GLN C 804 GLN C 856 ASN C1002 GLN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19847 Z= 0.189 Angle : 0.498 8.242 26985 Z= 0.264 Chirality : 0.044 0.187 3225 Planarity : 0.004 0.073 3425 Dihedral : 7.439 73.716 3201 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.26 % Allowed : 7.11 % Favored : 91.62 % 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: 0.86 (0.17), residues: 2383 helix: 2.77 (0.21), residues: 605 sheet: 0.96 (0.21), residues: 566 loop : -0.81 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.022 0.001 PHE A 906 TYR 0.021 0.001 TYR C 904 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 2.036 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6718 (t70) REVERT: A 88 ASP cc_start: 0.7570 (m-30) cc_final: 0.7348 (m-30) REVERT: A 544 ASN cc_start: 0.7336 (m110) cc_final: 0.6992 (m-40) REVERT: A 820 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: A 1138 TYR cc_start: 0.7075 (m-80) cc_final: 0.6765 (m-80) REVERT: B 282 ASN cc_start: 0.6613 (m-40) cc_final: 0.5531 (t0) REVERT: B 558 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7301 (mmmm) REVERT: B 1010 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7180 (pt0) REVERT: C 50 SER cc_start: 0.8823 (t) cc_final: 0.8557 (m) REVERT: C 658 ASN cc_start: 0.7159 (m110) cc_final: 0.6919 (m-40) REVERT: C 723 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7563 (p) REVERT: C 773 GLU cc_start: 0.7679 (tt0) cc_final: 0.7460 (tt0) outliers start: 27 outliers final: 11 residues processed: 189 average time/residue: 1.1120 time to fit residues: 241.8297 Evaluate side-chains 171 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.0040 chunk 184 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 969 ASN A1101 HIS ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 901 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19847 Z= 0.139 Angle : 0.471 8.428 26985 Z= 0.246 Chirality : 0.043 0.162 3225 Planarity : 0.003 0.059 3425 Dihedral : 6.263 57.557 3201 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.31 % Allowed : 9.31 % Favored : 89.38 % 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: 0.98 (0.17), residues: 2383 helix: 2.99 (0.21), residues: 605 sheet: 1.00 (0.21), residues: 561 loop : -0.78 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 886 HIS 0.002 0.000 HIS A1088 PHE 0.018 0.001 PHE C 86 TYR 0.018 0.001 TYR C 369 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 2.107 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6660 (t70) REVERT: A 88 ASP cc_start: 0.7496 (m-30) cc_final: 0.7287 (m-30) REVERT: A 190 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6071 (mpt-90) REVERT: A 544 ASN cc_start: 0.7460 (m110) cc_final: 0.7078 (m-40) REVERT: A 1138 TYR cc_start: 0.6894 (m-80) cc_final: 0.6568 (m-80) REVERT: B 282 ASN cc_start: 0.6507 (m-40) cc_final: 0.5397 (t0) REVERT: B 558 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7326 (mmmm) REVERT: B 1010 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7156 (pt0) REVERT: C 658 ASN cc_start: 0.7154 (m110) cc_final: 0.6911 (m-40) REVERT: C 723 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (p) REVERT: C 773 GLU cc_start: 0.7598 (tt0) cc_final: 0.7397 (tt0) outliers start: 28 outliers final: 11 residues processed: 184 average time/residue: 1.1545 time to fit residues: 244.7782 Evaluate side-chains 171 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 105 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 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 52 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19847 Z= 0.140 Angle : 0.460 8.656 26985 Z= 0.241 Chirality : 0.043 0.222 3225 Planarity : 0.003 0.051 3425 Dihedral : 5.590 57.764 3201 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.87 % Allowed : 10.67 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2383 helix: 3.02 (0.21), residues: 611 sheet: 1.02 (0.21), residues: 573 loop : -0.75 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.000 HIS C1083 PHE 0.017 0.001 PHE C 86 TYR 0.017 0.001 TYR C 369 ARG 0.002 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 2.079 Fit side-chains revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6726 (t70) REVERT: A 544 ASN cc_start: 0.7231 (m110) cc_final: 0.6853 (m-40) REVERT: A 820 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: A 856 ASN cc_start: 0.7278 (m110) cc_final: 0.7022 (m110) REVERT: A 1138 TYR cc_start: 0.6825 (m-80) cc_final: 0.6484 (m-80) REVERT: B 282 ASN cc_start: 0.6591 (m-40) cc_final: 0.5439 (t0) REVERT: B 287 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6830 (t0) REVERT: B 541 PHE cc_start: 0.6880 (p90) cc_final: 0.6636 (p90) REVERT: B 558 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7310 (mmmm) REVERT: B 1010 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7155 (pt0) REVERT: B 1113 GLN cc_start: 0.7992 (mp10) cc_final: 0.7649 (mp10) REVERT: C 658 ASN cc_start: 0.7164 (m110) cc_final: 0.6923 (m-40) REVERT: C 723 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 773 GLU cc_start: 0.7595 (tt0) cc_final: 0.7395 (tt0) outliers start: 40 outliers final: 23 residues processed: 190 average time/residue: 1.1332 time to fit residues: 247.3394 Evaluate side-chains 189 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 0.0970 chunk 201 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 762 GLN A 784 GLN A 969 ASN A1101 HIS A1135 ASN B 901 GLN B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19847 Z= 0.281 Angle : 0.529 8.425 26985 Z= 0.278 Chirality : 0.045 0.165 3225 Planarity : 0.004 0.047 3425 Dihedral : 5.835 59.698 3201 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 2.20 % Allowed : 11.93 % Favored : 85.87 % 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: 0.83 (0.17), residues: 2383 helix: 2.82 (0.21), residues: 599 sheet: 0.92 (0.21), residues: 558 loop : -0.84 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS C1083 PHE 0.021 0.002 PHE A 906 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 2.032 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6124 (mpt-90) REVERT: A 544 ASN cc_start: 0.7097 (m110) cc_final: 0.6699 (m-40) REVERT: A 820 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 856 ASN cc_start: 0.7575 (m110) cc_final: 0.7309 (m110) REVERT: A 969 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7826 (t0) REVERT: A 1138 TYR cc_start: 0.7063 (m-80) cc_final: 0.6719 (m-80) REVERT: B 541 PHE cc_start: 0.6913 (p90) cc_final: 0.6691 (p90) REVERT: B 558 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7344 (mmmm) REVERT: B 820 ASP cc_start: 0.8194 (m-30) cc_final: 0.7945 (m-30) REVERT: B 916 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7925 (tt) REVERT: B 1010 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7181 (pt0) REVERT: C 309 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: C 723 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7867 (p) REVERT: C 1092 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7481 (mm-30) outliers start: 47 outliers final: 24 residues processed: 195 average time/residue: 1.0487 time to fit residues: 237.3977 Evaluate side-chains 190 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 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 52 GLN A 762 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19847 Z= 0.183 Angle : 0.482 9.354 26985 Z= 0.253 Chirality : 0.043 0.186 3225 Planarity : 0.003 0.044 3425 Dihedral : 5.693 59.694 3201 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.80 % Rotamer: Outliers : 2.25 % Allowed : 12.59 % 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: 0.90 (0.17), residues: 2383 helix: 2.95 (0.21), residues: 599 sheet: 0.90 (0.21), residues: 563 loop : -0.80 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.016 0.001 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.001 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6101 (mpt-90) REVERT: A 544 ASN cc_start: 0.7071 (m110) cc_final: 0.6691 (m-40) REVERT: A 856 ASN cc_start: 0.7542 (m110) cc_final: 0.7267 (m110) REVERT: A 1002 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: A 1138 TYR cc_start: 0.6992 (m-80) cc_final: 0.6657 (m-80) REVERT: B 541 PHE cc_start: 0.6944 (p90) cc_final: 0.6700 (p90) REVERT: B 558 LYS cc_start: 0.7589 (mmmt) cc_final: 0.7324 (mmmm) REVERT: B 820 ASP cc_start: 0.8171 (m-30) cc_final: 0.7929 (m-30) REVERT: B 904 TYR cc_start: 0.7273 (m-10) cc_final: 0.6907 (m-10) REVERT: B 916 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (tt) REVERT: B 1010 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7179 (pt0) REVERT: C 723 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7934 (p) outliers start: 48 outliers final: 25 residues processed: 192 average time/residue: 1.0753 time to fit residues: 239.7337 Evaluate side-chains 186 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 0.0980 chunk 198 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 235 optimal weight: 0.0970 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19847 Z= 0.209 Angle : 0.499 11.690 26985 Z= 0.260 Chirality : 0.044 0.192 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.687 59.954 3201 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 2.11 % Allowed : 13.34 % Favored : 84.56 % 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: 0.85 (0.17), residues: 2383 helix: 2.89 (0.21), residues: 599 sheet: 0.81 (0.21), residues: 574 loop : -0.80 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.016 0.001 PHE C 86 TYR 0.019 0.001 TYR C1067 ARG 0.002 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 161 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.5691 (mpt-90) REVERT: A 544 ASN cc_start: 0.7066 (m110) cc_final: 0.6687 (m-40) REVERT: A 1002 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: A 1138 TYR cc_start: 0.7000 (m-80) cc_final: 0.6647 (m-80) REVERT: B 541 PHE cc_start: 0.6840 (p90) cc_final: 0.6585 (p90) REVERT: B 558 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7366 (mmmm) REVERT: B 902 MET cc_start: 0.8249 (mmp) cc_final: 0.7851 (mmp) REVERT: B 904 TYR cc_start: 0.7325 (m-10) cc_final: 0.6828 (m-10) REVERT: B 916 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7945 (tt) REVERT: B 1010 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7171 (pt0) REVERT: C 309 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: C 723 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7956 (p) REVERT: C 791 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8347 (t) outliers start: 45 outliers final: 27 residues processed: 186 average time/residue: 1.0972 time to fit residues: 236.0756 Evaluate side-chains 189 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19847 Z= 0.209 Angle : 0.499 10.392 26985 Z= 0.260 Chirality : 0.044 0.200 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.690 59.984 3201 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 2.11 % Allowed : 13.66 % Favored : 84.23 % 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: 0.87 (0.17), residues: 2383 helix: 2.95 (0.21), residues: 594 sheet: 0.81 (0.21), residues: 576 loop : -0.79 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.015 0.001 PHE C 86 TYR 0.019 0.001 TYR C1067 ARG 0.001 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 1.977 Fit side-chains REVERT: A 190 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.5684 (mpt-90) REVERT: A 544 ASN cc_start: 0.6882 (m110) cc_final: 0.6491 (m-40) REVERT: A 1002 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: A 1138 TYR cc_start: 0.7006 (m-80) cc_final: 0.6649 (m-80) REVERT: B 541 PHE cc_start: 0.6847 (p90) cc_final: 0.6592 (p90) REVERT: B 558 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7339 (mmmm) REVERT: B 904 TYR cc_start: 0.7325 (m-10) cc_final: 0.6679 (m-10) REVERT: B 916 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 1010 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7172 (pt0) REVERT: C 309 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6690 (tm-30) REVERT: C 790 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7915 (pttt) outliers start: 45 outliers final: 28 residues processed: 188 average time/residue: 1.0947 time to fit residues: 238.6376 Evaluate side-chains 186 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 207 optimal weight: 0.0870 chunk 218 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19847 Z= 0.230 Angle : 0.511 10.463 26985 Z= 0.267 Chirality : 0.044 0.195 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.759 59.872 3201 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.38 % Rotamer: Outliers : 1.87 % Allowed : 14.04 % Favored : 84.09 % 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: 0.81 (0.17), residues: 2383 helix: 2.88 (0.21), residues: 594 sheet: 0.80 (0.21), residues: 577 loop : -0.84 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.016 0.001 PHE C 86 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 2.185 Fit side-chains REVERT: A 190 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.5645 (mpt-90) REVERT: A 544 ASN cc_start: 0.6889 (m110) cc_final: 0.6497 (m-40) REVERT: A 1002 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: A 1138 TYR cc_start: 0.7092 (m-80) cc_final: 0.6732 (m-80) REVERT: B 541 PHE cc_start: 0.6863 (p90) cc_final: 0.6604 (p90) REVERT: B 558 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7394 (mmmm) REVERT: B 904 TYR cc_start: 0.7267 (m-10) cc_final: 0.6644 (m-10) REVERT: B 916 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 1010 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7191 (pt0) REVERT: C 275 PHE cc_start: 0.7937 (m-80) cc_final: 0.7639 (m-80) REVERT: C 309 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: C 790 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7931 (pttt) outliers start: 40 outliers final: 29 residues processed: 183 average time/residue: 1.1223 time to fit residues: 236.9841 Evaluate side-chains 189 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 784 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 901 GLN B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19847 Z= 0.248 Angle : 0.523 10.903 26985 Z= 0.273 Chirality : 0.045 0.198 3225 Planarity : 0.004 0.042 3425 Dihedral : 5.847 59.670 3201 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 1.64 % Allowed : 14.37 % Favored : 84.00 % 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: 0.74 (0.17), residues: 2383 helix: 2.82 (0.21), residues: 594 sheet: 0.71 (0.21), residues: 589 loop : -0.86 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 886 HIS 0.004 0.001 HIS C1083 PHE 0.015 0.001 PHE C 86 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG B1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4766 Ramachandran restraints generated. 2383 Oldfield, 0 Emsley, 2383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.107 Fit side-chains REVERT: A 190 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.5640 (mpt-90) REVERT: A 544 ASN cc_start: 0.6904 (m110) cc_final: 0.6512 (m-40) REVERT: A 1002 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: A 1138 TYR cc_start: 0.7151 (m-80) cc_final: 0.6776 (m-80) REVERT: B 558 LYS cc_start: 0.7673 (mmmt) cc_final: 0.7401 (mmmm) REVERT: B 564 GLN cc_start: 0.6692 (mm110) cc_final: 0.6487 (mm-40) REVERT: B 904 TYR cc_start: 0.7276 (m-10) cc_final: 0.6573 (m-10) REVERT: B 916 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 1010 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7193 (pt0) REVERT: C 309 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6700 (tm-30) REVERT: C 790 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7915 (pttt) outliers start: 35 outliers final: 28 residues processed: 184 average time/residue: 1.1202 time to fit residues: 238.4738 Evaluate side-chains 190 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 957 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 969 ASN C 564 GLN C 957 GLN C1002 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.180258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123435 restraints weight = 20735.039| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.07 r_work: 0.3204 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19847 Z= 0.316 Angle : 0.564 10.974 26985 Z= 0.295 Chirality : 0.046 0.215 3225 Planarity : 0.004 0.042 3425 Dihedral : 6.052 59.931 3201 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 1.68 % Allowed : 14.55 % Favored : 83.76 % 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: 0.57 (0.17), residues: 2383 helix: 2.72 (0.21), residues: 588 sheet: 0.64 (0.21), residues: 583 loop : -0.99 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 886 HIS 0.005 0.001 HIS C1083 PHE 0.014 0.002 PHE C 86 TYR 0.021 0.002 TYR C1067 ARG 0.003 0.000 ARG C1014 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5606.23 seconds wall clock time: 99 minutes 33.41 seconds (5973.41 seconds total)