Starting phenix.real_space_refine on Sun Feb 25 14:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z3z_14481/02_2024/7z3z_14481_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 16845 2.51 5 N 4311 2.21 5 O 5196 1.98 5 H 24780 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51252 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 16756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16756 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 53, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 16756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16756 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 53, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 16756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 16756 Classifications: {'peptide': 1089} Link IDs: {'PTRANS': 53, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 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: "H" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'NAG': 12, 'STE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'NAG': 12, 'STE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'NAG': 12, 'STE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 22.72, per 1000 atoms: 0.44 Number of scatterers: 51252 At special positions: 0 Unit cell: (138.61, 142.76, 175.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 5196 8.00 N 4311 7.00 C 16845 6.00 H 24780 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 42.88 Conformation dependent library (CDL) restraints added in 5.7 seconds 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 45 sheets defined 21.3% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.06 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.117A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.782A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 782 Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.835A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 914 through 939 removed outlier: 5.735A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.923A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.508A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1119 No H-bonds generated for 'chain 'A' and resid 1117 through 1119' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.814A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.117A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 738 through 741 No H-bonds generated for 'chain 'B' and resid 738 through 741' Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.783A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 782 Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.835A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 840 No H-bonds generated for 'chain 'B' and resid 837 through 840' Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 914 through 939 removed outlier: 5.735A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.922A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.508A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1119 No H-bonds generated for 'chain 'B' and resid 1117 through 1119' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.815A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.117A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 738 through 741 No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.782A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 Processing helix chain 'C' and resid 817 through 825 removed outlier: 3.835A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 840 No H-bonds generated for 'chain 'C' and resid 837 through 840' Processing helix chain 'C' and resid 849 through 854 Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 914 through 939 removed outlier: 5.735A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.923A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.509A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1119 No H-bonds generated for 'chain 'C' and resid 1117 through 1119' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.815A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.788A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.614A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 141 through 143 Processing sheet with id= E, first strand: chain 'A' and resid 311 through 314 Processing sheet with id= F, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.290A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 472 through 474 Processing sheet with id= I, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.121A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 670 through 675 Processing sheet with id= K, first strand: chain 'A' and resid 712 through 715 Processing sheet with id= L, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.011A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= N, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= O, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= P, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.788A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 48 through 55 Processing sheet with id= R, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.615A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 141 through 143 Processing sheet with id= T, first strand: chain 'B' and resid 311 through 314 Processing sheet with id= U, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.291A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= W, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= X, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.121A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 670 through 675 Processing sheet with id= Z, first strand: chain 'B' and resid 712 through 715 Processing sheet with id= AA, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.011A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AC, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AD, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AE, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.788A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 48 through 55 Processing sheet with id= AG, first strand: chain 'C' and resid 168 through 170 removed outlier: 3.614A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= AI, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= AJ, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.291A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AL, first strand: chain 'C' and resid 472 through 474 Processing sheet with id= AM, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.122A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 670 through 675 Processing sheet with id= AO, first strand: chain 'C' and resid 712 through 715 Processing sheet with id= AP, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.011A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AR, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AS, first strand: chain 'C' and resid 1094 through 1097 846 hydrogen bonds defined for protein. 2385 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: 22.27 Time building geometry restraints manager: 43.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 24780 1.01 - 1.21: 0 1.21 - 1.42: 11273 1.42 - 1.62: 15634 1.62 - 1.82: 150 Bond restraints: 51837 Sorted by residual: bond pdb=" NH2 ARG A 319 " pdb="HH21 ARG A 319 " ideal model delta sigma weight residual 0.860 0.807 0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" CB GLN B 935 " pdb=" CG GLN B 935 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.33e+00 bond pdb=" CB GLN A 935 " pdb=" CG GLN A 935 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.31e+00 bond pdb=" CB GLN C 935 " pdb=" CG GLN C 935 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.27e+00 bond pdb=" CG GLN C1142 " pdb=" CD GLN C1142 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.33e+00 ... (remaining 51832 not shown) Histogram of bond angle deviations from ideal: 59.23 - 79.60: 27 79.60 - 99.98: 31 99.98 - 120.35: 77415 120.35 - 140.72: 15426 140.72 - 161.10: 2 Bond angle restraints: 92901 Sorted by residual: angle pdb=" C SER A 155 " pdb=" N GLU A 156 " pdb=" H GLU A 156 " ideal model delta sigma weight residual 123.71 68.13 55.59 3.00e+00 1.11e-01 3.43e+02 angle pdb=" CA GLU A 156 " pdb=" N GLU A 156 " pdb=" H GLU A 156 " ideal model delta sigma weight residual 113.41 59.23 54.18 3.00e+00 1.11e-01 3.26e+02 angle pdb=" CZ ARG A 319 " pdb=" NH1 ARG A 319 " pdb="HH11 ARG A 319 " ideal model delta sigma weight residual 120.00 161.10 -41.10 3.00e+00 1.11e-01 1.88e+02 angle pdb="HH11 ARG A 319 " pdb=" NH1 ARG A 319 " pdb="HH12 ARG A 319 " ideal model delta sigma weight residual 120.00 79.37 40.63 3.00e+00 1.11e-01 1.83e+02 angle pdb=" CZ ARG A 319 " pdb=" NH1 ARG A 319 " pdb="HH12 ARG A 319 " ideal model delta sigma weight residual 120.00 81.76 38.24 3.00e+00 1.11e-01 1.62e+02 ... (remaining 92896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 23721 17.71 - 35.41: 1498 35.41 - 53.12: 452 53.12 - 70.83: 143 70.83 - 88.54: 25 Dihedral angle restraints: 25839 sinusoidal: 14424 harmonic: 11415 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 170.48 -77.48 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 170.47 -77.47 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual 93.00 170.45 -77.45 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 25836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4344 0.340 - 0.680: 12 0.680 - 1.021: 0 1.021 - 1.361: 0 1.361 - 1.701: 3 Chirality restraints: 4359 Sorted by residual: chirality pdb=" CG LEU C 223 " pdb=" CB LEU C 223 " pdb=" CD1 LEU C 223 " pdb=" CD2 LEU C 223 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.23e+01 chirality pdb=" CG LEU B 223 " pdb=" CB LEU B 223 " pdb=" CD1 LEU B 223 " pdb=" CD2 LEU B 223 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.23e+01 chirality pdb=" CG LEU A 223 " pdb=" CB LEU A 223 " pdb=" CD1 LEU A 223 " pdb=" CD2 LEU A 223 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.21e+01 ... (remaining 4356 not shown) Planarity restraints: 7806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B1142 " -0.008 2.00e-02 2.50e+03 6.87e-02 7.07e+01 pdb=" CD GLN B1142 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B1142 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN B1142 " -0.121 2.00e-02 2.50e+03 pdb="HE21 GLN B1142 " -0.036 2.00e-02 2.50e+03 pdb="HE22 GLN B1142 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 319 " -0.488 9.50e-02 1.11e+02 1.64e-01 3.60e+01 pdb=" NE ARG B 319 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B 319 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 319 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 319 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG B 319 " -0.011 2.00e-02 2.50e+03 pdb="HH12 ARG B 319 " 0.017 2.00e-02 2.50e+03 pdb="HH21 ARG B 319 " -0.024 2.00e-02 2.50e+03 pdb="HH22 ARG B 319 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 319 " 0.507 9.50e-02 1.11e+02 1.70e-01 3.46e+01 pdb=" NE ARG A 319 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 319 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 319 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 319 " 0.028 2.00e-02 2.50e+03 pdb="HH11 ARG A 319 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 319 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG A 319 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG A 319 " -0.026 2.00e-02 2.50e+03 ... (remaining 7803 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 545 2.02 - 2.67: 74157 2.67 - 3.31: 145071 3.31 - 3.96: 195215 3.96 - 4.60: 306415 Nonbonded interactions: 721403 Sorted by model distance: nonbonded pdb=" H GLU A 156 " pdb=" HA GLU A 156 " model vdw 1.380 1.816 nonbonded pdb=" O PRO B1053 " pdb="HE21 GLN B1054 " model vdw 1.603 1.850 nonbonded pdb=" O PRO C1053 " pdb="HE21 GLN C1054 " model vdw 1.604 1.850 nonbonded pdb=" O PRO A1053 " pdb="HE21 GLN A1054 " model vdw 1.604 1.850 nonbonded pdb=" HB3 LEU C 23 " pdb=" HG LEU C 23 " model vdw 1.613 1.952 ... (remaining 721398 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.630 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: 0.820 Extract box with map and model: 34.520 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 165.400 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.480 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.004 0.062 27057 Z= 0.286 Angle : 0.629 17.633 36804 Z= 0.302 Chirality : 0.067 1.701 4359 Planarity : 0.007 0.225 4674 Dihedral : 12.963 88.535 10734 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Rotamer: Outliers : 0.53 % Allowed : 0.42 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3231 helix: 1.28 (0.20), residues: 744 sheet: 0.42 (0.20), residues: 690 loop : -1.33 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 886 HIS 0.002 0.000 HIS A 655 PHE 0.039 0.001 PHE A 140 TYR 0.010 0.001 TYR B 160 ARG 0.011 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 198 average time/residue: 1.0153 time to fit residues: 307.4234 Evaluate side-chains 164 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain C residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27057 Z= 0.285 Angle : 0.557 15.147 36804 Z= 0.286 Chirality : 0.080 1.790 4359 Planarity : 0.003 0.068 4674 Dihedral : 6.559 59.937 4950 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.25 % Allowed : 3.24 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3231 helix: 1.54 (0.20), residues: 720 sheet: 0.40 (0.19), residues: 726 loop : -1.20 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 886 HIS 0.003 0.001 HIS C 66 PHE 0.012 0.001 PHE C 92 TYR 0.019 0.001 TYR A 170 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 PHE cc_start: 0.8287 (t80) cc_final: 0.8081 (t80) REVERT: B 388 ASN cc_start: 0.8299 (m110) cc_final: 0.7956 (m-40) outliers start: 7 outliers final: 7 residues processed: 177 average time/residue: 1.0129 time to fit residues: 271.1263 Evaluate side-chains 163 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 318 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 236 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27057 Z= 0.253 Angle : 0.526 14.110 36804 Z= 0.269 Chirality : 0.078 1.765 4359 Planarity : 0.003 0.028 4674 Dihedral : 6.298 59.052 4941 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 0.21 % Allowed : 4.23 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3231 helix: 1.63 (0.20), residues: 702 sheet: 0.37 (0.19), residues: 723 loop : -1.19 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.002 0.001 HIS A 66 PHE 0.010 0.001 PHE A 898 TYR 0.012 0.001 TYR B1067 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 4.130 Fit side-chains REVERT: A 388 ASN cc_start: 0.8332 (m110) cc_final: 0.8003 (m-40) REVERT: B 388 ASN cc_start: 0.8320 (m110) cc_final: 0.7957 (m-40) REVERT: C 388 ASN cc_start: 0.8263 (m110) cc_final: 0.7963 (m-40) outliers start: 6 outliers final: 5 residues processed: 171 average time/residue: 1.0400 time to fit residues: 269.1106 Evaluate side-chains 162 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 313 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 125 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27057 Z= 0.287 Angle : 0.530 14.494 36804 Z= 0.270 Chirality : 0.079 1.771 4359 Planarity : 0.003 0.026 4674 Dihedral : 6.113 58.197 4941 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 0.28 % Allowed : 4.62 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3231 helix: 1.63 (0.20), residues: 702 sheet: 0.28 (0.19), residues: 723 loop : -1.22 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS A1048 PHE 0.011 0.001 PHE A 898 TYR 0.013 0.001 TYR B1067 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 4.687 Fit side-chains REVERT: A 388 ASN cc_start: 0.8379 (m110) cc_final: 0.8017 (m-40) REVERT: B 388 ASN cc_start: 0.8364 (m110) cc_final: 0.8041 (m-40) REVERT: C 388 ASN cc_start: 0.8298 (m110) cc_final: 0.7975 (m-40) outliers start: 8 outliers final: 7 residues processed: 168 average time/residue: 1.0622 time to fit residues: 270.9859 Evaluate side-chains 165 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 4.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 281 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27057 Z= 0.378 Angle : 0.550 14.492 36804 Z= 0.281 Chirality : 0.080 1.787 4359 Planarity : 0.003 0.026 4674 Dihedral : 6.175 59.406 4941 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.21 % Allowed : 4.93 % Favored : 94.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3231 helix: 1.64 (0.20), residues: 684 sheet: 0.04 (0.19), residues: 720 loop : -1.18 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 PHE 0.012 0.001 PHE C 823 TYR 0.013 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 4.160 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 157 average time/residue: 1.0815 time to fit residues: 256.1132 Evaluate side-chains 149 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.5980 chunk 282 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 183 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 313 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 164 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27057 Z= 0.198 Angle : 0.514 14.629 36804 Z= 0.261 Chirality : 0.078 1.760 4359 Planarity : 0.003 0.028 4674 Dihedral : 5.888 59.957 4941 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.25 % Allowed : 5.43 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3231 helix: 1.81 (0.21), residues: 681 sheet: 0.19 (0.19), residues: 711 loop : -1.02 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS B 66 PHE 0.010 0.001 PHE A 898 TYR 0.012 0.001 TYR B 170 ARG 0.001 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 161 average time/residue: 1.0603 time to fit residues: 257.7720 Evaluate side-chains 154 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 312 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27057 Z= 0.290 Angle : 0.524 14.678 36804 Z= 0.265 Chirality : 0.079 1.772 4359 Planarity : 0.003 0.027 4674 Dihedral : 5.806 59.140 4941 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 3231 helix: 1.75 (0.21), residues: 687 sheet: 0.10 (0.19), residues: 720 loop : -1.04 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.001 HIS A1048 PHE 0.010 0.001 PHE C 823 TYR 0.012 0.001 TYR B1067 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 162 average time/residue: 1.0260 time to fit residues: 250.7004 Evaluate side-chains 158 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 chunk 245 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27057 Z= 0.217 Angle : 0.504 14.759 36804 Z= 0.253 Chirality : 0.078 1.768 4359 Planarity : 0.003 0.028 4674 Dihedral : 5.620 57.694 4940 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.21 % Allowed : 5.74 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3231 helix: 1.88 (0.21), residues: 684 sheet: 0.14 (0.19), residues: 717 loop : -0.98 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.002 0.001 HIS A 66 PHE 0.016 0.001 PHE C 157 TYR 0.011 0.001 TYR C 170 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 163 average time/residue: 1.0605 time to fit residues: 261.5995 Evaluate side-chains 154 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 chunk 291 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27057 Z= 0.266 Angle : 0.515 14.876 36804 Z= 0.260 Chirality : 0.079 1.769 4359 Planarity : 0.003 0.026 4674 Dihedral : 5.592 56.556 4939 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.28 % Allowed : 5.92 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3231 helix: 1.87 (0.21), residues: 684 sheet: 0.10 (0.19), residues: 717 loop : -0.98 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.002 0.001 HIS A1064 PHE 0.013 0.001 PHE B 140 TYR 0.011 0.001 TYR C 170 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 160 average time/residue: 1.0146 time to fit residues: 246.0737 Evaluate side-chains 158 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 145 optimal weight: 0.2980 chunk 213 optimal weight: 0.4980 chunk 322 optimal weight: 0.5980 chunk 297 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 27057 Z= 0.245 Angle : 0.642 59.197 36804 Z= 0.352 Chirality : 0.078 1.763 4359 Planarity : 0.003 0.031 4674 Dihedral : 5.586 56.532 4938 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.28 % Allowed : 5.88 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3231 helix: 1.89 (0.21), residues: 684 sheet: 0.11 (0.19), residues: 717 loop : -0.98 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.002 0.001 HIS A1064 PHE 0.012 0.001 PHE A 823 TYR 0.011 0.001 TYR B1067 ARG 0.001 0.000 ARG B 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 158 average time/residue: 1.0203 time to fit residues: 246.1810 Evaluate side-chains 157 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.8980 chunk 273 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.078589 restraints weight = 111361.752| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.40 r_work: 0.2753 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 27057 Z= 0.245 Angle : 0.641 59.050 36804 Z= 0.352 Chirality : 0.078 1.763 4359 Planarity : 0.003 0.031 4674 Dihedral : 5.586 56.532 4938 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.28 % Allowed : 5.88 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3231 helix: 1.89 (0.21), residues: 684 sheet: 0.11 (0.19), residues: 717 loop : -0.98 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.002 0.001 HIS A1064 PHE 0.012 0.001 PHE A 823 TYR 0.011 0.001 TYR B1067 ARG 0.001 0.000 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9832.22 seconds wall clock time: 176 minutes 26.70 seconds (10586.70 seconds total)