Starting phenix.real_space_refine on Sun Jul 5 02:48:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub0_26433/07_2026/7ub0_26433.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.003 sd= 0.154 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 15950 2.51 5 N 4092 2.21 5 O 4837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24993 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8152 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 50, 'TRANS': 991} Chain breaks: 6 Chain: "B" Number of atoms: 8031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8031 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Chain: "C" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8110 Classifications: {'peptide': 1039} Link IDs: {'PTRANS': 49, 'TRANS': 989} Chain breaks: 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.41, per 1000 atoms: 0.22 Number of scatterers: 24993 At special positions: 0 Unit cell: (129.6, 140.4, 174.96, 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 4837 8.00 N 4092 7.00 C 15950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 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=2.03 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=2.04 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=2.02 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 165 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 234 " " NAG D 1 " - " ASN A 801 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5818 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 45 sheets defined 26.7% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.825A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.946A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.648A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.636A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 857 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.264A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 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: 3.589A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.834A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.804A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.878A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.383A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 842 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.863A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.184A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.828A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.061A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.158A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.564A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.090A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.324A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.544A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.901A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.634A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.792A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.576A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.537A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.672A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' 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 1032 removed outlier: 3.563A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.100A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.491A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.470A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.921A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.156A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.869A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.728A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.590A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.648A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.506A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.839A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.241A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.812A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.846A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.856A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.714A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.287A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.607A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.275A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.577A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.560A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.619A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.651A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.565A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.588A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.212A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.605A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.549A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.812A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.341A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2919 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: 6.44 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7933 1.35 - 1.47: 6455 1.47 - 1.59: 11016 1.59 - 1.71: 0 1.71 - 1.84: 141 Bond restraints: 25545 Sorted by residual: bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 25540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 33585 1.25 - 2.51: 909 2.51 - 3.76: 223 3.76 - 5.01: 11 5.01 - 6.27: 10 Bond angle restraints: 34738 Sorted by residual: angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 108.54 5.86 2.30e+00 1.89e-01 6.48e+00 angle pdb=" C ARG B 102 " pdb=" N GLY B 103 " pdb=" CA GLY B 103 " ideal model delta sigma weight residual 121.22 116.13 5.09 2.05e+00 2.38e-01 6.18e+00 angle pdb=" N VAL A 620 " pdb=" CA VAL A 620 " pdb=" C VAL A 620 " ideal model delta sigma weight residual 108.88 113.95 -5.07 2.16e+00 2.14e-01 5.51e+00 angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.05e+00 angle pdb=" CB GLN A 173 " pdb=" CG GLN A 173 " pdb=" CD GLN A 173 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.05e+00 ... (remaining 34733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13452 17.89 - 35.78: 1147 35.78 - 53.67: 179 53.67 - 71.56: 30 71.56 - 89.44: 14 Dihedral angle restraints: 14822 sinusoidal: 5777 harmonic: 9045 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -168.87 82.87 1 1.00e+01 1.00e-02 8.41e+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 -158.96 72.96 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.35 71.35 1 1.00e+01 1.00e-02 6.53e+01 ... (remaining 14819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2939 0.042 - 0.084: 756 0.084 - 0.125: 373 0.125 - 0.167: 20 0.167 - 0.209: 4 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C2 NAG C1310 " pdb=" C1 NAG C1310 " pdb=" C3 NAG C1310 " pdb=" N2 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 4089 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 295 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 738 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C CYS C 738 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS C 738 " -0.011 2.00e-02 2.50e+03 pdb=" N THR C 739 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2076 2.74 - 3.28: 22740 3.28 - 3.82: 40571 3.82 - 4.36: 47447 4.36 - 4.90: 85556 Nonbonded interactions: 198390 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.205 3.040 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A1100 " pdb=" O7 NAG G 1 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.248 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.279 3.040 ... (remaining 198385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 68 or resid 81 through 137 or resid 166 through \ 210 or resid 215 through 243 or resid 263 through 621 or resid 641 through 674 \ or resid 691 through 1146 or resid 1303 through 1310)) selection = (chain 'B' and (resid 24 through 137 or resid 166 through 621 or resid 641 throu \ gh 1308)) selection = (chain 'C' and (resid 24 through 68 or resid 81 through 177 or resid 187 through \ 210 or resid 215 through 243 or resid 263 through 621 or resid 641 through 674 \ or resid 691 through 1146 or resid 1303 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.140 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25637 Z= 0.161 Angle : 0.527 6.265 34972 Z= 0.266 Chirality : 0.044 0.209 4092 Planarity : 0.004 0.050 4423 Dihedral : 13.201 89.444 8878 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3065 helix: 1.41 (0.19), residues: 713 sheet: 0.39 (0.18), residues: 720 loop : -0.99 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 559 TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (25545) covalent geometry : angle 0.51492 / 0.26 (34738) SS BOND : bond 0.00391 / 0.28 ( 42) SS BOND : angle 1.20654 / 0.90 ( 84) hydrogen bonds : bond 0.07925 / 5.21 ( 1051) hydrogen bonds : angle 5.49375 / 3.87 ( 2919) link_BETA1-4 : bond 0.00429 / 0.24 ( 10) link_BETA1-4 : angle 1.33275 / 0.86 ( 30) link_NAG-ASN : bond 0.00192 / 0.13 ( 40) link_NAG-ASN : angle 1.63348 / 1.12 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.008 Fit side-chains REVERT: B 468 ILE cc_start: 0.8943 (pt) cc_final: 0.8581 (tp) REVERT: B 1029 MET cc_start: 0.9355 (tpp) cc_final: 0.8984 (tpp) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1508 time to fit residues: 16.8590 Evaluate side-chains 51 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN B 613 GLN B 901 GLN C 901 GLN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.079572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054703 restraints weight = 64335.041| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.64 r_work: 0.2690 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 25637 Z= 0.296 Angle : 0.618 9.407 34972 Z= 0.318 Chirality : 0.048 0.205 4092 Planarity : 0.004 0.046 4423 Dihedral : 4.503 19.031 3331 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3065 helix: 1.53 (0.20), residues: 711 sheet: 0.19 (0.18), residues: 722 loop : -1.03 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.026 0.002 TYR C1067 PHE 0.022 0.002 PHE B 559 TRP 0.014 0.002 TRP C 436 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 (25545) covalent geometry : angle 0.60651 / 0.31 (34738) SS BOND : bond 0.00510 / 0.33 ( 42) SS BOND : angle 1.38084 / 1.07 ( 84) hydrogen bonds : bond 0.05644 / 3.66 ( 1051) hydrogen bonds : angle 5.44789 / 3.84 ( 2919) link_BETA1-4 : bond 0.00314 / 0.17 ( 10) link_BETA1-4 : angle 1.22882 / 0.82 ( 30) link_NAG-ASN : bond 0.00317 / 0.22 ( 40) link_NAG-ASN : angle 1.80530 / 1.20 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 1.003 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.1452 time to fit residues: 13.4353 Evaluate side-chains 47 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain C residue 200 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 143 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 414 GLN C 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056664 restraints weight = 64120.579| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.76 r_work: 0.2682 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25637 Z= 0.171 Angle : 0.514 9.461 34972 Z= 0.264 Chirality : 0.044 0.237 4092 Planarity : 0.003 0.036 4423 Dihedral : 4.244 18.193 3331 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 6.60 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3065 helix: 1.80 (0.20), residues: 721 sheet: 0.22 (0.18), residues: 720 loop : -0.97 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.021 0.001 TYR C1067 PHE 0.015 0.001 PHE B 559 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (25545) covalent geometry : angle 0.50326 / 0.26 (34738) SS BOND : bond 0.00401 / 0.26 ( 42) SS BOND : angle 1.12130 / 0.82 ( 84) hydrogen bonds : bond 0.04645 / 3.01 ( 1051) hydrogen bonds : angle 5.21672 / 3.67 ( 2919) link_BETA1-4 : bond 0.00314 / 0.17 ( 10) link_BETA1-4 : angle 1.07591 / 0.69 ( 30) link_NAG-ASN : bond 0.00197 / 0.14 ( 40) link_NAG-ASN : angle 1.59351 / 1.07 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8071 (t80) cc_final: 0.7865 (t80) outliers start: 15 outliers final: 10 residues processed: 62 average time/residue: 0.1386 time to fit residues: 16.0704 Evaluate side-chains 55 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 755 GLN Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 123 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 293 optimal weight: 6.9990 chunk 210 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN A 804 GLN A 935 GLN A1002 GLN C 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.056044 restraints weight = 64676.760| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.73 r_work: 0.2652 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 25637 Z= 0.298 Angle : 0.610 9.516 34972 Z= 0.311 Chirality : 0.047 0.234 4092 Planarity : 0.004 0.039 4423 Dihedral : 4.497 19.825 3331 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.78 % Allowed : 7.82 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3065 helix: 1.67 (0.20), residues: 712 sheet: 0.04 (0.18), residues: 723 loop : -1.05 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1014 TYR 0.024 0.002 TYR C1067 PHE 0.016 0.002 PHE A1121 TRP 0.012 0.001 TRP C 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.30 (25545) covalent geometry : angle 0.59849 / 0.31 (34738) SS BOND : bond 0.00530 / 0.33 ( 42) SS BOND : angle 1.36796 / 1.08 ( 84) hydrogen bonds : bond 0.05537 / 3.59 ( 1051) hydrogen bonds : angle 5.41259 / 3.80 ( 2919) link_BETA1-4 : bond 0.00282 / 0.17 ( 10) link_BETA1-4 : angle 1.21288 / 0.77 ( 30) link_NAG-ASN : bond 0.00319 / 0.23 ( 40) link_NAG-ASN : angle 1.80222 / 1.21 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 375 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: A 377 PHE cc_start: 0.8197 (t80) cc_final: 0.7993 (t80) outliers start: 21 outliers final: 12 residues processed: 67 average time/residue: 0.1455 time to fit residues: 17.6078 Evaluate side-chains 58 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 69 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 304 optimal weight: 0.5980 chunk 269 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057945 restraints weight = 63532.329| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.70 r_work: 0.2719 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25637 Z= 0.099 Angle : 0.471 9.527 34972 Z= 0.242 Chirality : 0.043 0.252 4092 Planarity : 0.003 0.034 4423 Dihedral : 4.024 17.136 3331 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.44 % Allowed : 8.71 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3065 helix: 2.07 (0.20), residues: 721 sheet: 0.22 (0.18), residues: 738 loop : -0.91 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (25545) covalent geometry : angle 0.46060 / 0.24 (34738) SS BOND : bond 0.00347 / 0.24 ( 42) SS BOND : angle 1.02712 / 0.77 ( 84) hydrogen bonds : bond 0.03980 / 2.57 ( 1051) hydrogen bonds : angle 5.00494 / 3.52 ( 2919) link_BETA1-4 : bond 0.00419 / 0.24 ( 10) link_BETA1-4 : angle 0.99850 / 0.63 ( 30) link_NAG-ASN : bond 0.00243 / 0.17 ( 40) link_NAG-ASN : angle 1.46061 / 0.99 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 1.001 Fit side-chains REVERT: A 375 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: A 377 PHE cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: C 486 PHE cc_start: 0.8997 (t80) cc_final: 0.8623 (t80) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1351 time to fit residues: 14.9499 Evaluate side-chains 55 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 45 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 0.0370 chunk 27 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.081903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.058387 restraints weight = 63798.386| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.71 r_work: 0.2731 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25637 Z= 0.101 Angle : 0.457 9.664 34972 Z= 0.233 Chirality : 0.043 0.249 4092 Planarity : 0.003 0.032 4423 Dihedral : 3.829 16.748 3331 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.70 % Allowed : 8.93 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3065 helix: 2.23 (0.20), residues: 721 sheet: 0.32 (0.18), residues: 727 loop : -0.83 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.016 0.001 TYR C1067 PHE 0.011 0.001 PHE A1121 TRP 0.010 0.001 TRP B 436 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (25545) covalent geometry : angle 0.44732 / 0.23 (34738) SS BOND : bond 0.00337 / 0.23 ( 42) SS BOND : angle 0.92976 / 0.67 ( 84) hydrogen bonds : bond 0.03811 / 2.46 ( 1051) hydrogen bonds : angle 4.85581 / 3.41 ( 2919) link_BETA1-4 : bond 0.00359 / 0.20 ( 10) link_BETA1-4 : angle 1.01442 / 0.66 ( 30) link_NAG-ASN : bond 0.00192 / 0.13 ( 40) link_NAG-ASN : angle 1.40938 / 0.96 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.977 Fit side-chains REVERT: A 135 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.2685 (m-10) REVERT: A 375 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: A 377 PHE cc_start: 0.8082 (t80) cc_final: 0.7848 (t80) REVERT: B 1029 MET cc_start: 0.9431 (tpp) cc_final: 0.9069 (tpp) REVERT: C 486 PHE cc_start: 0.8988 (t80) cc_final: 0.8621 (t80) outliers start: 19 outliers final: 12 residues processed: 68 average time/residue: 0.1400 time to fit residues: 17.4941 Evaluate side-chains 60 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 231 optimal weight: 0.0970 chunk 212 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057390 restraints weight = 63903.115| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.69 r_work: 0.2710 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 25637 Z= 0.150 Angle : 0.500 13.907 34972 Z= 0.253 Chirality : 0.044 0.246 4092 Planarity : 0.003 0.032 4423 Dihedral : 3.931 21.358 3331 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.82 % Allowed : 9.34 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3065 helix: 2.12 (0.20), residues: 721 sheet: 0.27 (0.18), residues: 731 loop : -0.83 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.018 0.001 TYR C1067 PHE 0.014 0.001 PHE A1121 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (25545) covalent geometry : angle 0.48614 / 0.25 (34738) SS BOND : bond 0.00354 / 0.23 ( 42) SS BOND : angle 1.64894 / 1.14 ( 84) hydrogen bonds : bond 0.04256 / 2.75 ( 1051) hydrogen bonds : angle 4.97741 / 3.49 ( 2919) link_BETA1-4 : bond 0.00309 / 0.17 ( 10) link_BETA1-4 : angle 1.06794 / 0.69 ( 30) link_NAG-ASN : bond 0.00192 / 0.13 ( 40) link_NAG-ASN : angle 1.46722 / 0.99 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 0.733 Fit side-chains REVERT: A 135 PHE cc_start: 0.4854 (OUTLIER) cc_final: 0.2545 (m-10) REVERT: A 375 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: A 377 PHE cc_start: 0.8142 (t80) cc_final: 0.7906 (t80) REVERT: C 486 PHE cc_start: 0.9006 (t80) cc_final: 0.8612 (t80) outliers start: 22 outliers final: 17 residues processed: 68 average time/residue: 0.1330 time to fit residues: 16.6322 Evaluate side-chains 65 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 286 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.080919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057755 restraints weight = 63881.538| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.70 r_work: 0.2700 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25637 Z= 0.154 Angle : 0.497 10.637 34972 Z= 0.252 Chirality : 0.044 0.246 4092 Planarity : 0.003 0.032 4423 Dihedral : 3.955 17.173 3331 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.93 % Allowed : 9.52 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3065 helix: 2.09 (0.20), residues: 721 sheet: 0.27 (0.18), residues: 736 loop : -0.84 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1014 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE A1121 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (25545) covalent geometry : angle 0.48420 / 0.25 (34738) SS BOND : bond 0.00378 / 0.24 ( 42) SS BOND : angle 1.46605 / 1.06 ( 84) hydrogen bonds : bond 0.04330 / 2.79 ( 1051) hydrogen bonds : angle 4.98895 / 3.51 ( 2919) link_BETA1-4 : bond 0.00310 / 0.17 ( 10) link_BETA1-4 : angle 1.07860 / 0.70 ( 30) link_NAG-ASN : bond 0.00185 / 0.13 ( 40) link_NAG-ASN : angle 1.48283 / 1.01 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.930 Fit side-chains REVERT: A 135 PHE cc_start: 0.4940 (OUTLIER) cc_final: 0.2588 (m-10) REVERT: A 375 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: A 377 PHE cc_start: 0.8087 (t80) cc_final: 0.7851 (t80) REVERT: C 486 PHE cc_start: 0.9007 (t80) cc_final: 0.8615 (t80) outliers start: 25 outliers final: 19 residues processed: 71 average time/residue: 0.1318 time to fit residues: 17.3414 Evaluate side-chains 67 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 154 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 233 optimal weight: 0.0770 chunk 277 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055743 restraints weight = 64587.950| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.71 r_work: 0.2664 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25637 Z= 0.257 Angle : 0.572 10.436 34972 Z= 0.291 Chirality : 0.046 0.242 4092 Planarity : 0.003 0.035 4423 Dihedral : 4.243 18.219 3331 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.07 % Allowed : 9.56 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3065 helix: 1.90 (0.20), residues: 721 sheet: 0.13 (0.18), residues: 733 loop : -0.95 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.022 0.001 TYR C1067 PHE 0.016 0.002 PHE B 759 TRP 0.009 0.001 TRP C 436 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 (25545) covalent geometry : angle 0.55934 / 0.29 (34738) SS BOND : bond 0.00469 / 0.30 ( 42) SS BOND : angle 1.56648 / 1.18 ( 84) hydrogen bonds : bond 0.05152 / 3.33 ( 1051) hydrogen bonds : angle 5.23925 / 3.68 ( 2919) link_BETA1-4 : bond 0.00248 / 0.13 ( 10) link_BETA1-4 : angle 1.18609 / 0.75 ( 30) link_NAG-ASN : bond 0.00279 / 0.20 ( 40) link_NAG-ASN : angle 1.68201 / 1.13 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 47 time to evaluate : 0.966 Fit side-chains REVERT: A 135 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.2852 (m-10) REVERT: A 375 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 377 PHE cc_start: 0.8161 (t80) cc_final: 0.7948 (t80) REVERT: C 486 PHE cc_start: 0.9011 (t80) cc_final: 0.8622 (t80) outliers start: 29 outliers final: 21 residues processed: 75 average time/residue: 0.1340 time to fit residues: 18.6149 Evaluate side-chains 68 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 127 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055959 restraints weight = 64533.440| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.72 r_work: 0.2670 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25637 Z= 0.224 Angle : 0.549 10.046 34972 Z= 0.279 Chirality : 0.045 0.244 4092 Planarity : 0.003 0.034 4423 Dihedral : 4.247 18.440 3331 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.93 % Allowed : 9.78 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3065 helix: 1.88 (0.20), residues: 715 sheet: 0.08 (0.18), residues: 731 loop : -0.98 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1014 TYR 0.022 0.001 TYR C1067 PHE 0.015 0.001 PHE B 759 TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.22 (25545) covalent geometry : angle 0.53644 / 0.28 (34738) SS BOND : bond 0.00455 / 0.29 ( 42) SS BOND : angle 1.49318 / 1.15 ( 84) hydrogen bonds : bond 0.04915 / 3.17 ( 1051) hydrogen bonds : angle 5.22298 / 3.67 ( 2919) link_BETA1-4 : bond 0.00277 / 0.15 ( 10) link_BETA1-4 : angle 1.16641 / 0.73 ( 30) link_NAG-ASN : bond 0.00247 / 0.18 ( 40) link_NAG-ASN : angle 1.65249 / 1.12 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6130 Ramachandran restraints generated. 3065 Oldfield, 0 Emsley, 3065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 135 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.2780 (m-10) REVERT: A 375 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: A 377 PHE cc_start: 0.8137 (t80) cc_final: 0.7933 (t80) outliers start: 25 outliers final: 21 residues processed: 69 average time/residue: 0.1396 time to fit residues: 17.9917 Evaluate side-chains 68 residues out of total 2699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 218 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.058492 restraints weight = 63733.277| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.75 r_work: 0.2718 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25637 Z= 0.099 Angle : 0.468 9.739 34972 Z= 0.238 Chirality : 0.043 0.252 4092 Planarity : 0.003 0.033 4423 Dihedral : 3.910 16.963 3331 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.78 % Allowed : 10.08 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3065 helix: 2.15 (0.20), residues: 722 sheet: 0.22 (0.18), residues: 740 loop : -0.82 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 905 TYR 0.018 0.001 TYR A 170 PHE 0.012 0.001 PHE B 759 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (25545) covalent geometry : angle 0.45793 / 0.24 (34738) SS BOND : bond 0.00366 / 0.24 ( 42) SS BOND : angle 1.13606 / 0.81 ( 84) hydrogen bonds : bond 0.03872 / 2.49 ( 1051) hydrogen bonds : angle 4.92843 / 3.47 ( 2919) link_BETA1-4 : bond 0.00382 / 0.21 ( 10) link_BETA1-4 : angle 1.02997 / 0.65 ( 30) link_NAG-ASN : bond 0.00214 / 0.15 ( 40) link_NAG-ASN : angle 1.42749 / 0.97 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4506.80 seconds wall clock time: 78 minutes 36.83 seconds (4716.83 seconds total)