Starting phenix.real_space_refine on Tue Mar 19 16:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6l_24879/03_2024/7s6l_24879.pdb" } resolution = 4.0 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= 0.024 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 114 5.16 5 C 15773 2.51 5 N 4070 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24755 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7688 Classifications: {'peptide': 984} Link IDs: {'PTRANS': 53, 'TRANS': 930} Chain breaks: 9 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 755 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "B" Number of atoms: 7436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7436 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 51, 'TRANS': 897} Chain breaks: 13 Chain: "C" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7509 Classifications: {'peptide': 961} Link IDs: {'PTRANS': 52, 'TRANS': 908} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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: "G" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" 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: "K" 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.83, per 1000 atoms: 0.56 Number of scatterers: 24755 At special positions: 0 Unit cell: (129.95, 139.15, 233.45, 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 114 16.00 O 4798 8.00 N 4070 7.00 C 15773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.11 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 343 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B1134 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1098 " Time building additional restraints: 9.10 Conformation dependent library (CDL) restraints added in 7.3 seconds 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5848 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 51 sheets defined 25.9% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.733A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.936A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.754A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 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: 3.777A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.515A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.724A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.870A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.189A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 5.072A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.468A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 737 through 744 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: 3.625A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.827A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 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: 3.505A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.968A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.572A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.518A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR B 323 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASN B 542 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.518A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.594A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.417A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.227A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.047A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.319A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.533A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.609A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.647A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.647A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1123 Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.583A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.706A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.239A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.443A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.615A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.571A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 714 through 715 Processing sheet with id=AD6, first strand: chain 'B' and resid 719 through 728 removed outlier: 6.345A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD9, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.898A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.035A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.315A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.913A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.470A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.752A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.040A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.040A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.601A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.648A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.835A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.275A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.275A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.756A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3072 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: 11.25 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6598 1.33 - 1.48: 8123 1.48 - 1.62: 10421 1.62 - 1.77: 37 1.77 - 1.91: 119 Bond restraints: 25298 Sorted by residual: bond pdb=" CB LEU B 242 " pdb=" CG LEU B 242 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" CG TYR A 200 " pdb=" CD1 TYR A 200 " ideal model delta sigma weight residual 1.389 1.516 -0.127 2.10e-02 2.27e+03 3.66e+01 bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.392 -0.066 1.10e-02 8.26e+03 3.56e+01 bond pdb=" CG TYR B 200 " pdb=" CD1 TYR B 200 " ideal model delta sigma weight residual 1.389 1.513 -0.124 2.10e-02 2.27e+03 3.47e+01 ... (remaining 25293 not shown) Histogram of bond angle deviations from ideal: 95.35 - 108.47: 2581 108.47 - 121.58: 25866 121.58 - 134.70: 5963 134.70 - 147.82: 0 147.82 - 160.94: 1 Bond angle restraints: 34411 Sorted by residual: angle pdb=" C2 NAG B1302 " pdb=" N2 NAG B1302 " pdb=" C7 NAG B1302 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C PRO B 792 " pdb=" N PRO B 793 " pdb=" CA PRO B 793 " ideal model delta sigma weight residual 119.56 128.09 -8.53 1.01e+00 9.80e-01 7.13e+01 angle pdb=" C ILE H 52 " pdb=" N PRO H 52A" pdb=" CA PRO H 52A" ideal model delta sigma weight residual 119.56 128.10 -8.54 1.02e+00 9.61e-01 7.00e+01 angle pdb=" C ASP A1139 " pdb=" N PRO A1140 " pdb=" CA PRO A1140 " ideal model delta sigma weight residual 119.56 128.03 -8.47 1.02e+00 9.61e-01 6.89e+01 angle pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.56 127.92 -8.36 1.02e+00 9.61e-01 6.71e+01 ... (remaining 34406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 14987 17.86 - 35.72: 365 35.72 - 53.57: 85 53.57 - 71.43: 44 71.43 - 89.29: 25 Dihedral angle restraints: 15506 sinusoidal: 6441 harmonic: 9065 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 161.40 -68.40 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 159.46 -66.46 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -143.69 57.69 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 15503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 3005 0.112 - 0.223: 802 0.223 - 0.335: 138 0.335 - 0.446: 54 0.446 - 0.558: 15 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.77e+01 ... (remaining 4011 not shown) Planarity restraints: 4428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 801 " 0.093 2.00e-02 2.50e+03 9.76e-02 1.19e+02 pdb=" CG ASN B 801 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 801 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 801 " -0.151 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.090 2.00e-02 2.50e+03 9.41e-02 1.11e+02 pdb=" CG ASN B 616 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.146 2.00e-02 2.50e+03 pdb=" C1 NAG B1301 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.077 2.00e-02 2.50e+03 8.22e-02 8.45e+01 pdb=" CG ASN A 616 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.129 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.100 2.00e-02 2.50e+03 ... (remaining 4425 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7893 2.85 - 3.36: 23278 3.36 - 3.87: 43222 3.87 - 4.39: 51527 4.39 - 4.90: 81919 Nonbonded interactions: 207839 Sorted by model distance: nonbonded pdb=" N ALA C 520 " pdb=" O ALA C 520 " model vdw 2.336 2.496 nonbonded pdb=" NZ LYS B 557 " pdb=" OD2 ASP B 574 " model vdw 2.395 2.520 nonbonded pdb=" N ALA A 520 " pdb=" O ALA A 520 " model vdw 2.401 2.496 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.426 2.496 nonbonded pdb=" OD2 ASP A 571 " pdb=" NZ LYS C 964 " model vdw 2.429 2.520 ... (remaining 207834 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 66 or resid 82 through 113 or resid 116 through \ 134 or resid 166 through 263 or resid 265 through 323 or resid 327 through 442 \ or resid 448 through 454 or resid 462 through 470 or resid 491 through 500 or re \ sid 503 through 676 or resid 690 through 826 or resid 856 through 1147 or resid \ 1301 through 1304)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 210 or resid 215 through \ 454 or resid 462 through 470 or resid 491 through 826 or resid 856 through 1147 \ or resid 1301 through 1304)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 113 or resid 116 through \ 134 or resid 166 through 196 or resid 200 through 210 or resid 215 through 323 \ or resid 327 through 442 or resid 448 through 500 or resid 503 through 826 or re \ sid 856 through 1147 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.600 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 69.880 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 : 0.020 0.127 25298 Z= 1.280 Angle : 1.738 36.379 34411 Z= 1.171 Chirality : 0.113 0.558 4014 Planarity : 0.009 0.050 4405 Dihedral : 9.975 89.290 9541 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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 (0.14), residues: 3043 helix: 0.26 (0.18), residues: 681 sheet: 1.09 (0.19), residues: 641 loop : 0.49 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.012 TRP H 103 HIS 0.008 0.002 HIS H 100G PHE 0.045 0.006 PHE L 98 TYR 0.079 0.010 TYR B1067 ARG 0.007 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9254 (mt) cc_final: 0.9020 (tp) REVERT: A 489 TYR cc_start: 0.5384 (m-80) cc_final: 0.5134 (m-80) REVERT: A 759 PHE cc_start: 0.8910 (t80) cc_final: 0.8609 (t80) REVERT: A 869 MET cc_start: 0.9497 (mtm) cc_final: 0.9034 (mtp) REVERT: H 48 MET cc_start: 0.6001 (mtp) cc_final: 0.5263 (mpp) REVERT: H 58 MET cc_start: 0.2865 (mpt) cc_final: 0.1882 (tmm) REVERT: H 79 TYR cc_start: 0.8740 (m-80) cc_final: 0.8085 (m-80) REVERT: H 81 GLU cc_start: 0.8369 (tt0) cc_final: 0.8007 (tm-30) REVERT: B 195 LYS cc_start: 0.8831 (pttt) cc_final: 0.8480 (tmtt) REVERT: B 740 MET cc_start: 0.8844 (tpt) cc_final: 0.8353 (tpp) REVERT: B 781 VAL cc_start: 0.9657 (t) cc_final: 0.9331 (m) REVERT: B 1029 MET cc_start: 0.8790 (ttm) cc_final: 0.8551 (tmm) REVERT: C 40 ASP cc_start: 0.9184 (t0) cc_final: 0.8767 (p0) REVERT: C 406 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8355 (mm-30) REVERT: C 759 PHE cc_start: 0.8354 (t80) cc_final: 0.8004 (t80) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.3960 time to fit residues: 96.9400 Evaluate side-chains 72 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 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 207 HIS A 804 GLN A 914 ASN A 935 GLN A1005 GLN A1010 GLN A1048 HIS L 89 GLN B 613 GLN B 955 ASN B1005 GLN B1011 GLN B1048 HIS C 207 HIS C 613 GLN C 895 GLN C 955 ASN C1011 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25298 Z= 0.228 Angle : 0.651 9.712 34411 Z= 0.347 Chirality : 0.046 0.287 4014 Planarity : 0.004 0.038 4405 Dihedral : 5.605 50.935 3954 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 0.55 % Allowed : 2.60 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.01 (0.15), residues: 3043 helix: 1.91 (0.20), residues: 669 sheet: 0.77 (0.18), residues: 751 loop : 0.18 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 886 HIS 0.005 0.001 HIS C 655 PHE 0.029 0.002 PHE C 338 TYR 0.029 0.002 TYR B1067 ARG 0.004 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9454 (mt) cc_final: 0.9216 (mp) REVERT: A 489 TYR cc_start: 0.4905 (m-80) cc_final: 0.4418 (m-80) REVERT: A 697 MET cc_start: 0.7808 (ptm) cc_final: 0.7556 (ptm) REVERT: A 869 MET cc_start: 0.9376 (mtm) cc_final: 0.8934 (mtm) REVERT: A 900 MET cc_start: 0.9198 (mtp) cc_final: 0.8929 (mtt) REVERT: H 58 MET cc_start: 0.3455 (mpt) cc_final: 0.2231 (tmm) REVERT: H 79 TYR cc_start: 0.8766 (m-80) cc_final: 0.8194 (m-80) REVERT: H 81 GLU cc_start: 0.8560 (tt0) cc_final: 0.8235 (tm-30) REVERT: B 390 LEU cc_start: 0.8648 (mm) cc_final: 0.8442 (mm) REVERT: B 436 TRP cc_start: 0.7241 (t60) cc_final: 0.6478 (t60) REVERT: B 731 MET cc_start: 0.8642 (ttm) cc_final: 0.8419 (ttm) REVERT: B 781 VAL cc_start: 0.9517 (t) cc_final: 0.9113 (m) REVERT: B 869 MET cc_start: 0.9446 (mtp) cc_final: 0.8994 (mtp) REVERT: C 40 ASP cc_start: 0.9164 (t0) cc_final: 0.8857 (p0) REVERT: C 406 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8271 (mm-30) REVERT: C 805 ILE cc_start: 0.9460 (mp) cc_final: 0.9230 (tp) outliers start: 15 outliers final: 3 residues processed: 95 average time/residue: 0.3489 time to fit residues: 55.6636 Evaluate side-chains 63 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 888 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 0.0470 chunk 87 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 251 optimal weight: 0.0470 chunk 279 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1005 GLN A1011 GLN A1113 GLN B 957 GLN B1113 GLN C 121 ASN C1005 GLN C1113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25298 Z= 0.147 Angle : 0.560 12.632 34411 Z= 0.293 Chirality : 0.044 0.384 4014 Planarity : 0.004 0.034 4405 Dihedral : 4.940 53.012 3954 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.17 % Favored : 97.80 % Rotamer: Outliers : 0.73 % Allowed : 2.63 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.96 (0.15), residues: 3043 helix: 2.20 (0.20), residues: 658 sheet: 0.55 (0.18), residues: 743 loop : 0.10 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 35 HIS 0.004 0.001 HIS C 655 PHE 0.039 0.001 PHE A 759 TYR 0.026 0.001 TYR B1067 ARG 0.004 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9503 (mt) cc_final: 0.9279 (mp) REVERT: A 489 TYR cc_start: 0.4965 (m-80) cc_final: 0.4492 (m-80) REVERT: A 697 MET cc_start: 0.7821 (ptm) cc_final: 0.7571 (ptm) REVERT: A 869 MET cc_start: 0.9222 (mtm) cc_final: 0.8964 (mtt) REVERT: A 900 MET cc_start: 0.9120 (mtp) cc_final: 0.8883 (mtt) REVERT: A 1029 MET cc_start: 0.9595 (tpp) cc_final: 0.9338 (tpp) REVERT: H 48 MET cc_start: 0.5086 (mtt) cc_final: 0.4602 (mpp) REVERT: H 58 MET cc_start: 0.3205 (mpt) cc_final: 0.1941 (ttt) REVERT: H 79 TYR cc_start: 0.8687 (m-80) cc_final: 0.8230 (m-80) REVERT: B 697 MET cc_start: 0.8464 (pmm) cc_final: 0.8083 (pmm) REVERT: B 740 MET cc_start: 0.9121 (tpp) cc_final: 0.8905 (tpp) REVERT: B 869 MET cc_start: 0.9424 (mtp) cc_final: 0.8846 (mtp) REVERT: C 40 ASP cc_start: 0.9122 (t0) cc_final: 0.8841 (p0) REVERT: C 406 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8225 (mm-30) REVERT: C 697 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: C 805 ILE cc_start: 0.9398 (mp) cc_final: 0.9148 (tp) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 0.3864 time to fit residues: 53.1433 Evaluate side-chains 61 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 189 optimal weight: 0.0970 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS B1023 ASN C 81 ASN C 641 ASN C 655 HIS C 935 GLN C 954 GLN C1048 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 25298 Z= 0.297 Angle : 0.622 9.284 34411 Z= 0.320 Chirality : 0.043 0.157 4014 Planarity : 0.004 0.042 4405 Dihedral : 4.947 51.360 3954 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.66 % Allowed : 3.73 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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 (0.15), residues: 3043 helix: 2.16 (0.20), residues: 656 sheet: 0.39 (0.18), residues: 767 loop : 0.06 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP L 35 HIS 0.007 0.002 HIS B1064 PHE 0.027 0.002 PHE C 759 TYR 0.022 0.002 TYR B 369 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9601 (mt) cc_final: 0.9372 (mp) REVERT: A 489 TYR cc_start: 0.4852 (m-80) cc_final: 0.4371 (m-80) REVERT: A 697 MET cc_start: 0.7829 (ptm) cc_final: 0.7538 (ptm) REVERT: A 869 MET cc_start: 0.9398 (mtm) cc_final: 0.9092 (mtt) REVERT: A 1029 MET cc_start: 0.9652 (tpp) cc_final: 0.9347 (tpp) REVERT: H 48 MET cc_start: 0.5052 (mtt) cc_final: 0.4509 (mpp) REVERT: H 58 MET cc_start: 0.3286 (mpt) cc_final: 0.1944 (ttt) REVERT: H 79 TYR cc_start: 0.8687 (m-80) cc_final: 0.8015 (m-80) REVERT: B 697 MET cc_start: 0.8527 (pmm) cc_final: 0.8006 (pmm) REVERT: B 731 MET cc_start: 0.8692 (ttm) cc_final: 0.8483 (ttm) REVERT: B 740 MET cc_start: 0.9265 (tpp) cc_final: 0.9024 (tpp) REVERT: B 869 MET cc_start: 0.9451 (mtp) cc_final: 0.8829 (mtm) REVERT: B 1029 MET cc_start: 0.9522 (tpp) cc_final: 0.9287 (tpp) REVERT: C 40 ASP cc_start: 0.9208 (t0) cc_final: 0.8681 (p0) REVERT: C 406 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8279 (mm-30) REVERT: C 697 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: C 763 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9523 (mt) REVERT: C 869 MET cc_start: 0.9485 (mtm) cc_final: 0.8633 (mtm) outliers start: 18 outliers final: 10 residues processed: 68 average time/residue: 0.3973 time to fit residues: 45.0683 Evaluate side-chains 61 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 268 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A1119 ASN L 37 GLN L 53 ASN B 655 HIS B1088 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25298 Z= 0.268 Angle : 0.572 14.018 34411 Z= 0.295 Chirality : 0.043 0.171 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.924 52.649 3954 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 0.84 % Allowed : 3.99 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.76 (0.15), residues: 3043 helix: 2.12 (0.21), residues: 666 sheet: 0.45 (0.18), residues: 751 loop : -0.09 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 35 HIS 0.005 0.001 HIS A1048 PHE 0.052 0.002 PHE B 718 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 49 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9634 (mt) cc_final: 0.9399 (mp) REVERT: A 489 TYR cc_start: 0.4840 (m-80) cc_final: 0.4395 (m-80) REVERT: A 697 MET cc_start: 0.7821 (ptm) cc_final: 0.7491 (ptm) REVERT: A 869 MET cc_start: 0.9381 (mtm) cc_final: 0.9180 (mtt) REVERT: A 1029 MET cc_start: 0.9716 (tpp) cc_final: 0.9452 (tpp) REVERT: H 19 LYS cc_start: 0.7806 (pptt) cc_final: 0.7602 (tppt) REVERT: H 58 MET cc_start: 0.3451 (mpt) cc_final: 0.2272 (ttt) REVERT: L 4 MET cc_start: 0.3452 (mtt) cc_final: 0.3229 (mmt) REVERT: B 697 MET cc_start: 0.8547 (pmm) cc_final: 0.8262 (pmm) REVERT: B 740 MET cc_start: 0.9348 (tpp) cc_final: 0.9098 (tpp) REVERT: B 869 MET cc_start: 0.9442 (mtp) cc_final: 0.8893 (mtp) REVERT: B 1029 MET cc_start: 0.9346 (tpp) cc_final: 0.9116 (tpp) REVERT: C 40 ASP cc_start: 0.9101 (t0) cc_final: 0.8454 (p0) REVERT: C 697 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8304 (ttp) outliers start: 23 outliers final: 15 residues processed: 67 average time/residue: 0.3778 time to fit residues: 42.7402 Evaluate side-chains 61 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 25298 Z= 0.340 Angle : 0.624 9.266 34411 Z= 0.318 Chirality : 0.043 0.181 4014 Planarity : 0.004 0.039 4405 Dihedral : 5.111 50.972 3954 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 0.80 % Allowed : 4.72 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3043 helix: 1.99 (0.20), residues: 667 sheet: 0.26 (0.18), residues: 756 loop : -0.25 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.006 0.002 HIS C 49 PHE 0.086 0.002 PHE B 718 TYR 0.019 0.002 TYR C1067 ARG 0.004 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9639 (mt) cc_final: 0.9406 (mp) REVERT: A 489 TYR cc_start: 0.4871 (m-80) cc_final: 0.4418 (m-80) REVERT: A 697 MET cc_start: 0.7960 (ptm) cc_final: 0.7613 (ptm) REVERT: A 869 MET cc_start: 0.9435 (mtm) cc_final: 0.9188 (mtt) REVERT: A 1029 MET cc_start: 0.9701 (tpp) cc_final: 0.9411 (tpp) REVERT: H 48 MET cc_start: 0.4573 (OUTLIER) cc_final: 0.4073 (mpp) REVERT: H 58 MET cc_start: 0.3489 (mpt) cc_final: 0.2297 (ttt) REVERT: H 79 TYR cc_start: 0.7494 (m-80) cc_final: 0.7263 (m-80) REVERT: B 697 MET cc_start: 0.8619 (pmm) cc_final: 0.8251 (pmm) REVERT: B 740 MET cc_start: 0.9402 (tpp) cc_final: 0.9167 (tpp) REVERT: B 869 MET cc_start: 0.9449 (mtp) cc_final: 0.8944 (mtp) REVERT: C 40 ASP cc_start: 0.9118 (t0) cc_final: 0.8318 (p0) REVERT: C 697 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8393 (ttp) REVERT: C 979 ASP cc_start: 0.9511 (m-30) cc_final: 0.9308 (t0) outliers start: 22 outliers final: 15 residues processed: 66 average time/residue: 0.3909 time to fit residues: 44.5652 Evaluate side-chains 63 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN A 949 GLN A 953 ASN A1088 HIS B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25298 Z= 0.206 Angle : 0.519 8.398 34411 Z= 0.269 Chirality : 0.042 0.185 4014 Planarity : 0.004 0.041 4405 Dihedral : 4.866 52.652 3954 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 0.69 % Allowed : 4.97 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.71 (0.15), residues: 3043 helix: 2.31 (0.21), residues: 666 sheet: 0.31 (0.19), residues: 736 loop : -0.18 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 35 HIS 0.004 0.001 HIS A1048 PHE 0.088 0.001 PHE B 718 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9660 (mt) cc_final: 0.9416 (mp) REVERT: A 489 TYR cc_start: 0.4832 (m-80) cc_final: 0.4361 (m-80) REVERT: A 697 MET cc_start: 0.7868 (ptm) cc_final: 0.7504 (ptm) REVERT: A 869 MET cc_start: 0.9395 (mtm) cc_final: 0.9163 (mtt) REVERT: A 1029 MET cc_start: 0.9717 (tpp) cc_final: 0.9437 (tpp) REVERT: H 48 MET cc_start: 0.4701 (OUTLIER) cc_final: 0.4392 (mpp) REVERT: H 58 MET cc_start: 0.3929 (mpt) cc_final: 0.2714 (ttt) REVERT: H 79 TYR cc_start: 0.7447 (m-80) cc_final: 0.7235 (m-80) REVERT: H 94 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5510 (mpp-170) REVERT: L 4 MET cc_start: 0.3613 (mtt) cc_final: 0.3248 (mmt) REVERT: B 697 MET cc_start: 0.8698 (pmm) cc_final: 0.8202 (pmm) REVERT: B 740 MET cc_start: 0.9420 (tpp) cc_final: 0.9199 (tpp) REVERT: B 869 MET cc_start: 0.9429 (mtp) cc_final: 0.9009 (mtp) REVERT: B 1029 MET cc_start: 0.9506 (tpp) cc_final: 0.9076 (tpp) REVERT: C 95 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8298 (m) REVERT: C 697 MET cc_start: 0.8638 (ttp) cc_final: 0.8376 (ttm) REVERT: C 979 ASP cc_start: 0.9469 (m-30) cc_final: 0.9265 (t0) outliers start: 19 outliers final: 13 residues processed: 68 average time/residue: 0.3792 time to fit residues: 43.8202 Evaluate side-chains 62 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 0.0170 chunk 234 optimal weight: 0.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1108 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25298 Z= 0.143 Angle : 0.498 16.106 34411 Z= 0.257 Chirality : 0.042 0.171 4014 Planarity : 0.003 0.036 4405 Dihedral : 4.557 52.662 3952 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.62 % Allowed : 5.52 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.82 (0.15), residues: 3043 helix: 2.47 (0.21), residues: 666 sheet: 0.32 (0.19), residues: 731 loop : -0.11 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 35 HIS 0.003 0.001 HIS C1048 PHE 0.027 0.001 PHE A 888 TYR 0.024 0.001 TYR B 369 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9647 (mt) cc_final: 0.9387 (mp) REVERT: A 351 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.8745 (p90) REVERT: A 489 TYR cc_start: 0.4836 (m-80) cc_final: 0.4364 (m-10) REVERT: A 697 MET cc_start: 0.7793 (ptm) cc_final: 0.7447 (ptm) REVERT: A 869 MET cc_start: 0.9325 (mtm) cc_final: 0.9118 (mtt) REVERT: A 1029 MET cc_start: 0.9714 (tpp) cc_final: 0.9419 (tpp) REVERT: H 48 MET cc_start: 0.4388 (OUTLIER) cc_final: 0.4162 (mpp) REVERT: H 58 MET cc_start: 0.3895 (mpt) cc_final: 0.2683 (ttt) REVERT: H 79 TYR cc_start: 0.7562 (m-80) cc_final: 0.7355 (m-80) REVERT: H 94 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5475 (mpp-170) REVERT: L 4 MET cc_start: 0.3241 (mtt) cc_final: 0.2990 (mmt) REVERT: B 697 MET cc_start: 0.8660 (pmm) cc_final: 0.8392 (pmm) REVERT: B 731 MET cc_start: 0.8485 (ttm) cc_final: 0.8244 (tpp) REVERT: B 740 MET cc_start: 0.9427 (tpp) cc_final: 0.9199 (tpp) REVERT: B 869 MET cc_start: 0.9422 (mtp) cc_final: 0.8995 (mtp) REVERT: B 1029 MET cc_start: 0.9450 (tpp) cc_final: 0.9049 (tpp) REVERT: C 979 ASP cc_start: 0.9465 (m-30) cc_final: 0.9263 (t0) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.4121 time to fit residues: 45.0485 Evaluate side-chains 59 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 251 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25298 Z= 0.272 Angle : 0.562 8.661 34411 Z= 0.288 Chirality : 0.042 0.217 4014 Planarity : 0.004 0.038 4405 Dihedral : 4.725 49.992 3952 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 0.69 % Allowed : 5.48 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.65 (0.15), residues: 3043 helix: 2.33 (0.21), residues: 666 sheet: 0.28 (0.18), residues: 756 loop : -0.25 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 35 HIS 0.005 0.001 HIS B1083 PHE 0.027 0.001 PHE B 718 TYR 0.048 0.002 TYR B1067 ARG 0.006 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 2.841 Fit side-chains revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9667 (mt) cc_final: 0.9420 (mp) REVERT: A 351 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8808 (p90) REVERT: A 489 TYR cc_start: 0.4928 (m-80) cc_final: 0.4453 (m-80) REVERT: A 697 MET cc_start: 0.7908 (ptm) cc_final: 0.7533 (ptm) REVERT: A 869 MET cc_start: 0.9406 (mtm) cc_final: 0.9187 (mtt) REVERT: A 1029 MET cc_start: 0.9723 (tpp) cc_final: 0.9415 (tpp) REVERT: H 48 MET cc_start: 0.4453 (OUTLIER) cc_final: 0.4214 (mpp) REVERT: H 58 MET cc_start: 0.3930 (mpt) cc_final: 0.2705 (ttt) REVERT: H 94 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5536 (mpp-170) REVERT: L 4 MET cc_start: 0.3891 (mtt) cc_final: 0.3507 (mmt) REVERT: B 697 MET cc_start: 0.8707 (pmm) cc_final: 0.8156 (pmm) REVERT: B 740 MET cc_start: 0.9461 (tpp) cc_final: 0.9236 (tpp) REVERT: B 869 MET cc_start: 0.9416 (mtp) cc_final: 0.9006 (mtp) REVERT: B 1005 GLN cc_start: 0.9684 (OUTLIER) cc_final: 0.9481 (mm-40) REVERT: B 1029 MET cc_start: 0.9529 (tpp) cc_final: 0.9219 (tpp) REVERT: B 1067 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7319 (t80) outliers start: 19 outliers final: 13 residues processed: 59 average time/residue: 0.3840 time to fit residues: 37.7982 Evaluate side-chains 61 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.9990 chunk 294 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 308 optimal weight: 0.5980 chunk 284 optimal weight: 2.9990 chunk 245 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 25298 Z= 0.139 Angle : 0.489 10.232 34411 Z= 0.254 Chirality : 0.042 0.168 4014 Planarity : 0.003 0.037 4405 Dihedral : 4.511 52.985 3952 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.66 % Allowed : 5.45 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.76 (0.15), residues: 3043 helix: 2.47 (0.21), residues: 667 sheet: 0.26 (0.18), residues: 736 loop : -0.16 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 35 HIS 0.003 0.001 HIS C1048 PHE 0.032 0.001 PHE B 888 TYR 0.038 0.001 TYR B1067 ARG 0.005 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6086 Ramachandran restraints generated. 3043 Oldfield, 0 Emsley, 3043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9668 (mt) cc_final: 0.9420 (mp) REVERT: A 489 TYR cc_start: 0.4969 (m-80) cc_final: 0.4490 (m-10) REVERT: A 697 MET cc_start: 0.7759 (ptm) cc_final: 0.7393 (ptm) REVERT: A 869 MET cc_start: 0.9334 (mtm) cc_final: 0.9126 (mtt) REVERT: A 1029 MET cc_start: 0.9715 (tpp) cc_final: 0.9439 (tpp) REVERT: H 58 MET cc_start: 0.3903 (mpt) cc_final: 0.2680 (ttt) REVERT: H 94 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5491 (mpp-170) REVERT: L 4 MET cc_start: 0.3775 (mtt) cc_final: 0.3389 (mmt) REVERT: B 697 MET cc_start: 0.8694 (pmm) cc_final: 0.8327 (pmm) REVERT: B 731 MET cc_start: 0.8516 (ttm) cc_final: 0.8272 (tpp) REVERT: B 740 MET cc_start: 0.9430 (tpp) cc_final: 0.9204 (tpp) REVERT: B 869 MET cc_start: 0.9409 (mtp) cc_final: 0.8992 (mtp) REVERT: B 1029 MET cc_start: 0.9462 (tpp) cc_final: 0.9067 (tpp) REVERT: B 1067 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.6802 (t80) outliers start: 18 outliers final: 11 residues processed: 61 average time/residue: 0.3788 time to fit residues: 39.1622 Evaluate side-chains 59 residues out of total 2735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain B residue 718 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.058181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.039261 restraints weight = 203254.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037003 restraints weight = 105989.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037222 restraints weight = 70835.800| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25298 Z= 0.233 Angle : 0.532 8.678 34411 Z= 0.273 Chirality : 0.042 0.178 4014 Planarity : 0.004 0.037 4405 Dihedral : 4.581 50.208 3952 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer: Outliers : 0.51 % Allowed : 5.74 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.71 (0.15), residues: 3043 helix: 2.41 (0.21), residues: 667 sheet: 0.28 (0.18), residues: 725 loop : -0.21 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 35 HIS 0.004 0.001 HIS B1083 PHE 0.033 0.001 PHE B 888 TYR 0.032 0.001 TYR B1067 ARG 0.007 0.000 ARG H 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.92 seconds wall clock time: 71 minutes 8.31 seconds (4268.31 seconds total)