Starting phenix.real_space_refine on Thu Mar 5 15:31:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpe_26052/03_2026/7tpe_26052.map" } resolution = 4.0 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= -0.005 sd= 0.123 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 100 5.16 5 C 14770 2.51 5 N 3834 2.21 5 O 4495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23199 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7700 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 48, 'TRANS': 956} Chain breaks: 10 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 7070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7070 Classifications: {'peptide': 975} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 46, 'TRANS': 928} Chain breaks: 10 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 479 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7617 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 48, 'TRANS': 954} Chain breaks: 8 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.44, per 1000 atoms: 0.23 Number of scatterers: 23199 At special positions: 0 Unit cell: (128.52, 137.16, 183.6, 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 100 16.00 O 4495 8.00 N 3834 7.00 C 14770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 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=2.04 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=2.02 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 C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.01 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 973.0 milliseconds 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5594 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 43 sheets defined 27.8% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.132A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.426A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 634 through 639 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.516A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.771A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.662A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.726A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 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: 3.565A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 removed outlier: 3.627A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.613A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) 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 1141 through 1146 removed outlier: 4.293A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 336 through 344 removed outlier: 4.161A pdb=" N GLY B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.465A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 403 through 411 removed outlier: 4.083A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.125A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.154A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.659A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.160A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 removed outlier: 3.964A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.780A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1143 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.938A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 619 through 623 removed outlier: 3.585A pdb=" N ALA C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.932A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 6.492A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.391A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.753A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.549A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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 removed outlier: 4.106A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 removed outlier: 3.893A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.204A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.561A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.602A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.157A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.907A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.760A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 452 removed outlier: 3.831A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.159A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 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 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.182A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.311A 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: 4.661A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.928A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.319A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.272A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.559A 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: 5.225A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.858A 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 356 removed outlier: 4.305A pdb=" N LYS B 356 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASP B 398 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.683A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.223A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N PHE C 220 " --> pdb=" O PRO C 209 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG C 34 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU C 223 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.585A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 310 through 319 removed outlier: 6.894A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.567A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.567A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.639A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.667A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.667A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 807 through 808 removed outlier: 3.730A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.447A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2721 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: 5.65 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6454 1.33 - 1.46: 4181 1.46 - 1.58: 12923 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 23682 Sorted by residual: bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C5 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 23677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23616 1.87 - 3.74: 7556 3.74 - 5.61: 997 5.61 - 7.47: 111 7.47 - 9.34: 17 Bond angle restraints: 32297 Sorted by residual: angle pdb=" CA PRO B 621 " pdb=" N PRO B 621 " pdb=" CD PRO B 621 " ideal model delta sigma weight residual 112.00 102.66 9.34 1.40e+00 5.10e-01 4.45e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.88 -6.08 1.00e+00 1.00e+00 3.70e+01 angle pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " pdb=" ND2 ASN B 122 " ideal model delta sigma weight residual 116.40 125.08 -8.68 1.50e+00 4.44e-01 3.35e+01 angle pdb=" CA PRO A 621 " pdb=" N PRO A 621 " pdb=" CD PRO A 621 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.13e+01 angle pdb=" CB HIS C 655 " pdb=" CG HIS C 655 " pdb=" CD2 HIS C 655 " ideal model delta sigma weight residual 131.20 124.13 7.07 1.30e+00 5.92e-01 2.96e+01 ... (remaining 32292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13735 17.90 - 35.79: 831 35.79 - 53.69: 153 53.69 - 71.59: 53 71.59 - 89.48: 21 Dihedral angle restraints: 14793 sinusoidal: 6133 harmonic: 8660 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -144.67 58.67 1 1.00e+01 1.00e-02 4.61e+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 -142.27 56.27 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA CYS C1126 " pdb=" C CYS C1126 " pdb=" N ASP C1127 " pdb=" CA ASP C1127 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2661 0.093 - 0.186: 1126 0.186 - 0.279: 142 0.279 - 0.372: 10 0.372 - 0.465: 4 Chirality restraints: 3943 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.13e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.84e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.08e+01 ... (remaining 3940 not shown) Planarity restraints: 4141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.131 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" CG ASN C1074 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.123 2.00e-02 2.50e+03 1.32e-01 2.18e+02 pdb=" CG ASN A 801 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.206 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 633 " 0.159 2.00e-02 2.50e+03 8.94e-02 2.00e+02 pdb=" CG TRP B 633 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP B 633 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 633 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP B 633 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP B 633 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 633 " -0.144 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 633 " 0.101 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 633 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 633 " 0.100 2.00e-02 2.50e+03 ... (remaining 4138 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11785 2.98 - 3.46: 23914 3.46 - 3.94: 38589 3.94 - 4.42: 42990 4.42 - 4.90: 70503 Nonbonded interactions: 187781 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.501 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.523 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.524 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.524 3.040 nonbonded pdb=" OD1 ASP C 627 " pdb=" OG SER C 637 " model vdw 2.539 3.040 ... (remaining 187776 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 197 or (resid 198 and (name N or name CA or name C o \ r name O or name CB )) or resid 199 through 210 or (resid 211 and (name N or nam \ e CA or name C or name O or name CB )) or resid 212 or (resid 213 and (name N or \ name CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 a \ nd (name N or name CA or name C or name O or name CB )) or resid 310 through 323 \ or (resid 324 and (name N or name CA or name C or name O or name CB )) or resid \ 325 through 332 or (resid 333 through 334 and (name N or name CA or name C or n \ ame O or name CB )) or resid 335 through 345 or (resid 346 through 360 and (name \ N or name CA or name C or name O or name CB )) or resid 361 or (resid 362 throu \ gh 378 and (name N or name CA or name C or name O or name CB )) or resid 379 or \ (resid 380 and (name N or name CA or name C or name O or name CB )) or resid 381 \ or (resid 382 through 383 and (name N or name CA or name C or name O or name CB \ )) or resid 384 or (resid 385 through 390 and (name N or name CA or name C or n \ ame O or name CB )) or resid 391 or (resid 392 through 403 and (name N or name C \ A or name C or name O or name CB )) or (resid 404 through 411 and (name N or nam \ e CA or name C or name O or name CB )) or resid 412 through 413 or (resid 414 th \ rough 415 and (name N or name CA or name C or name O or name CB )) or resid 416 \ or (resid 417 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 427 or (resid 428 through 430 and (name N or name CA or \ name C or name O or name CB )) or resid 431 through 432 or (resid 433 through 44 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 457 or (resi \ d 462 and (name N or name CA or name C or name O or name CB )) or resid 463 or ( \ resid 464 through 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 491 or (resid 492 through 495 and (name N or name CA or name C or name O \ or name CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or \ name C or name O or name CB )) or resid 499 or (resid 500 through 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (na \ me N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 thr \ ough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 5 through 528 or (resid 529 and (name N or name CA or name C or name O or name C \ B )) or resid 530 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or name \ CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or n \ ame CA or name C or name O or name CB )) or resid 797 through 810 or (resid 811 \ and (name N or name CA or name C or name O or name CB )) or resid 813 through 82 \ 7 or resid 856 through 866 or (resid 867 through 868 and (name N or name CA or n \ ame C or name O or name CB )) or resid 869 through 939 or (resid 940 and (name N \ or name CA or name C or name O or name CB )) or resid 941 through 984 or (resid \ 985 and (name N or name CA or name C or name O or name CB )) or resid 986 throu \ gh 987 or (resid 988 through 989 and (name N or name CA or name C or name O or n \ ame CB )) or resid 990 through 1141 or (resid 1142 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1143 through 1144 or (resid 1145 through 11 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 1147 throug \ h 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 197 or (resid 198 and (name N or name CA or name C or name O or name CB ) \ ) or resid 199 through 210 or (resid 211 and (name N or name CA or name C or nam \ e O or name CB )) or resid 212 or (resid 213 and (name N or name CA or name C or \ name O or name CB )) or resid 214 through 241 or (resid 242 through 263 and (na \ me N or name CA or name C or name O or name CB )) or resid 265 through 280 or (r \ esid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 t \ hrough 323 or (resid 324 and (name N or name CA or name C or name O or name CB ) \ ) or resid 325 through 442 or resid 452 or resid 462 through 501 or resid 503 th \ rough 567 or (resid 568 and (name N or name CA or name C or name O or name CB )) \ or resid 569 through 570 or (resid 571 and (name N or name CA or name C or name \ O or name CB )) or resid 572 through 581 or (resid 582 through 583 and (name N \ or name CA or name C or name O or name CB )) or resid 584 through 585 or (resid \ 586 and (name N or name CA or name C or name O or name CB )) or resid 587 throug \ h 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) or \ resid 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name \ CA or name C or name O or name CB )) or resid 746 through 810 or (resid 811 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 827 o \ r resid 856 through 866 or (resid 867 through 868 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 939 or (resid 94 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or re \ sid 986 through 987 or (resid 988 through 989 and (name N or name CA or name C o \ r name O or name CB )) or resid 990 through 1072 or (resid 1073 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid 11 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 1119 throug \ h 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O or \ name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 197 through 217 or (resid 218 and (name N o \ r name CA or name C or name O or name CB )) or resid 219 through 223 or (resid 2 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) or r \ esid 240 through 308 or (resid 309 and (name N or name CA or name C or name O or \ name CB )) or resid 310 through 332 or (resid 333 through 334 and (name N or na \ me CA or name C or name O or name CB )) or resid 335 through 344 or (resid 345 t \ hrough 360 and (name N or name CA or name C or name O or name CB )) or resid 361 \ or (resid 362 through 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 or (resid 382 through 383 and (name N or name CA or name C \ or name O or name CB )) or resid 384 or (resid 385 through 390 and (name N or na \ me CA or name C or name O or name CB )) or resid 391 or (resid 392 through 403 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 404 through 41 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or name \ CB )) or (resid 416 through 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 or (resid 427 through 430 and (name N or name CA or name \ C or name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and \ (name N or name CA or name C or name O or name CB )) or resid 452 or resid 462 \ through 463 or (resid 464 through 466 and (name N or name CA or name C or name O \ or name CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or \ name C or name O or name CB )) or resid 496 or (resid 497 through 498 and (name \ N or name CA or name C or name O or name CB )) or resid 499 through 500 or (resi \ d 501 and (name N or name CA or name C or name O or name CB )) or (resid 503 and \ (name N or name CA or name C or name O or name CB )) or (resid 504 through 506 \ and (name N or name CA or name C or name O or name CB )) or resid 507 or (resid \ 508 through 515 and (name N or name CA or name C or name O or name CB )) or (res \ id 522 through 524 and (name N or name CA or name C or name O or name CB )) or r \ esid 525 through 527 or (resid 528 through 529 and (name N or name CA or name C \ or name O or name CB )) or resid 530 through 553 or (resid 554 and (name N or na \ me CA or name C or name O or name CB )) or resid 555 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 570 \ or (resid 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 581 or (resid 582 through 583 and (name N or name CA or name C or n \ ame O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name C \ A or name C or name O or name CB )) or resid 587 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 645 or \ (resid 646 through 647 and (name N or name CA or name C or name O or name CB )) \ or resid 648 through 793 or (resid 794 and (name N or name CA or name C or name \ O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C or n \ ame O or name CB )) or resid 797 through 920 or (resid 921 and (name N or name C \ A or name C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and \ (name N or name CA or name C or name O or name CB )) or resid 1074 through 1117 \ or (resid 1118 and (name N or name CA or name C or name O or name CB )) or resi \ d 1119 through 1141 or (resid 1142 and (name N or name CA or name C or name O or \ name CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or \ name C or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.840 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.013 0.077 23777 Z= 0.754 Angle : 1.770 9.936 32545 Z= 1.149 Chirality : 0.094 0.465 3943 Planarity : 0.014 0.160 4095 Dihedral : 12.978 89.481 9088 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.59 % Favored : 90.31 % Rotamer: Outliers : 1.83 % Allowed : 3.19 % Favored : 94.98 % Cbeta Deviations : 0.21 % 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: -1.39 (0.14), residues: 2921 helix: -0.46 (0.17), residues: 659 sheet: -0.22 (0.23), residues: 449 loop : -1.31 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG B 328 TYR 0.120 0.022 TYR C 660 PHE 0.059 0.012 PHE C 58 TRP 0.161 0.029 TRP A 633 HIS 0.018 0.004 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01340 (23682) covalent geometry : angle 1.74290 (32297) SS BOND : bond 0.00941 ( 37) SS BOND : angle 1.75021 ( 74) hydrogen bonds : bond 0.15864 ( 989) hydrogen bonds : angle 8.60958 ( 2721) link_BETA1-4 : bond 0.02291 ( 12) link_BETA1-4 : angle 4.48917 ( 36) link_NAG-ASN : bond 0.01016 ( 46) link_NAG-ASN : angle 4.62645 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 38 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8627 (mtt) cc_final: 0.8410 (mtt) REVERT: C 628 GLN cc_start: 0.3812 (OUTLIER) cc_final: 0.2892 (tm-30) REVERT: C 1072 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8799 (pm20) outliers start: 43 outliers final: 17 residues processed: 80 average time/residue: 0.1674 time to fit residues: 21.5452 Evaluate side-chains 47 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 935 GLN A 969 ASN B 343 ASN B 764 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.045382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.030603 restraints weight = 251859.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.031521 restraints weight = 164796.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031309 restraints weight = 109435.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.031537 restraints weight = 99932.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.031494 restraints weight = 83761.345| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23777 Z= 0.167 Angle : 0.725 19.233 32545 Z= 0.373 Chirality : 0.046 0.310 3943 Planarity : 0.005 0.179 4095 Dihedral : 7.769 82.622 4410 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.07 % Favored : 94.80 % Rotamer: Outliers : 1.15 % Allowed : 4.56 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.04 % 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: -0.61 (0.15), residues: 2921 helix: 1.37 (0.20), residues: 662 sheet: -0.31 (0.20), residues: 587 loop : -1.21 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.017 0.002 TYR C 453 PHE 0.020 0.002 PHE A 186 TRP 0.018 0.002 TRP A 436 HIS 0.012 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00345 (23682) covalent geometry : angle 0.69211 (32297) SS BOND : bond 0.00397 ( 37) SS BOND : angle 1.17474 ( 74) hydrogen bonds : bond 0.05247 ( 989) hydrogen bonds : angle 6.49645 ( 2721) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 1.85921 ( 36) link_NAG-ASN : bond 0.00478 ( 46) link_NAG-ASN : angle 3.18467 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 628 GLN cc_start: 0.4606 (OUTLIER) cc_final: 0.3651 (tm-30) REVERT: C 740 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8896 (ttt) REVERT: C 869 MET cc_start: 0.9373 (mtp) cc_final: 0.9153 (mtp) REVERT: C 902 MET cc_start: 0.9571 (tpt) cc_final: 0.9285 (tpp) REVERT: C 1072 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8798 (pm20) outliers start: 27 outliers final: 14 residues processed: 58 average time/residue: 0.1576 time to fit residues: 15.4689 Evaluate side-chains 47 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 112 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 194 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 chunk 273 optimal weight: 2.9990 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.044780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.029844 restraints weight = 252551.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.030875 restraints weight = 166267.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.030729 restraints weight = 103174.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.030877 restraints weight = 96953.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.030911 restraints weight = 90289.607| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23777 Z= 0.194 Angle : 0.662 12.924 32545 Z= 0.338 Chirality : 0.044 0.338 3943 Planarity : 0.005 0.163 4095 Dihedral : 7.088 83.090 4402 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % Rotamer: Outliers : 1.36 % Allowed : 5.53 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.52 (0.15), residues: 2921 helix: 1.68 (0.20), residues: 660 sheet: -0.32 (0.20), residues: 569 loop : -1.22 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1107 TYR 0.021 0.002 TYR A 380 PHE 0.020 0.002 PHE A 377 TRP 0.022 0.002 TRP A 633 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00422 (23682) covalent geometry : angle 0.63757 (32297) SS BOND : bond 0.00363 ( 37) SS BOND : angle 1.04232 ( 74) hydrogen bonds : bond 0.04641 ( 989) hydrogen bonds : angle 6.15436 ( 2721) link_BETA1-4 : bond 0.00452 ( 12) link_BETA1-4 : angle 1.54937 ( 36) link_NAG-ASN : bond 0.00549 ( 46) link_NAG-ASN : angle 2.63595 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 30 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 986 LYS cc_start: 0.9734 (tttt) cc_final: 0.9340 (tptp) REVERT: C 628 GLN cc_start: 0.4773 (OUTLIER) cc_final: 0.3677 (tm-30) REVERT: C 1072 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8776 (pm20) outliers start: 32 outliers final: 21 residues processed: 62 average time/residue: 0.1535 time to fit residues: 16.1841 Evaluate side-chains 53 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 119 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 268 optimal weight: 0.0470 chunk 205 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 chunk 270 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 276 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN A 950 ASN A 954 GLN C 239 GLN C 625 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.044776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.029943 restraints weight = 252907.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.031008 restraints weight = 165852.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.030851 restraints weight = 101052.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.030991 restraints weight = 94768.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.031008 restraints weight = 89077.009| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23777 Z= 0.146 Angle : 0.592 12.604 32545 Z= 0.301 Chirality : 0.043 0.266 3943 Planarity : 0.005 0.162 4095 Dihedral : 6.587 84.299 4395 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 1.49 % Allowed : 6.64 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.35 (0.15), residues: 2921 helix: 1.96 (0.20), residues: 672 sheet: -0.27 (0.20), residues: 592 loop : -1.20 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.017 0.001 TYR A1067 PHE 0.016 0.001 PHE C 318 TRP 0.013 0.001 TRP A 633 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00319 (23682) covalent geometry : angle 0.56972 (32297) SS BOND : bond 0.00300 ( 37) SS BOND : angle 0.96377 ( 74) hydrogen bonds : bond 0.04052 ( 989) hydrogen bonds : angle 5.84694 ( 2721) link_BETA1-4 : bond 0.00383 ( 12) link_BETA1-4 : angle 1.36063 ( 36) link_NAG-ASN : bond 0.00385 ( 46) link_NAG-ASN : angle 2.39610 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 32 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9072 (mtp) cc_final: 0.8756 (ttt) REVERT: A 986 LYS cc_start: 0.9717 (tttt) cc_final: 0.9325 (tptp) REVERT: A 1029 MET cc_start: 0.8877 (tpt) cc_final: 0.8563 (tpt) REVERT: C 628 GLN cc_start: 0.4319 (OUTLIER) cc_final: 0.3216 (tm-30) REVERT: C 869 MET cc_start: 0.9261 (mtp) cc_final: 0.9048 (mtp) outliers start: 35 outliers final: 19 residues processed: 64 average time/residue: 0.1488 time to fit residues: 16.3605 Evaluate side-chains 50 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 23 optimal weight: 10.0000 chunk 197 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 274 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 35 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN A1125 ASN B 641 ASN B1048 HIS B1125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.044371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029290 restraints weight = 252144.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.030342 restraints weight = 169528.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030124 restraints weight = 103832.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030286 restraints weight = 100585.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.030317 restraints weight = 91508.334| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23777 Z= 0.244 Angle : 0.676 12.656 32545 Z= 0.340 Chirality : 0.044 0.272 3943 Planarity : 0.005 0.162 4095 Dihedral : 6.656 89.937 4389 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.78 % Favored : 93.05 % Rotamer: Outliers : 1.66 % Allowed : 7.58 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.58 (0.15), residues: 2921 helix: 1.78 (0.20), residues: 672 sheet: -0.52 (0.19), residues: 635 loop : -1.31 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1039 TYR 0.018 0.002 TYR A 266 PHE 0.015 0.002 PHE C 318 TRP 0.013 0.002 TRP B 64 HIS 0.006 0.002 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.00527 (23682) covalent geometry : angle 0.65430 (32297) SS BOND : bond 0.00357 ( 37) SS BOND : angle 1.05676 ( 74) hydrogen bonds : bond 0.04441 ( 989) hydrogen bonds : angle 6.04201 ( 2721) link_BETA1-4 : bond 0.00483 ( 12) link_BETA1-4 : angle 1.53261 ( 36) link_NAG-ASN : bond 0.00669 ( 46) link_NAG-ASN : angle 2.49968 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 31 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9346 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: A 471 GLU cc_start: 0.9575 (OUTLIER) cc_final: 0.9309 (pp20) REVERT: A 1029 MET cc_start: 0.8897 (tpt) cc_final: 0.8502 (tpt) REVERT: C 628 GLN cc_start: 0.4656 (OUTLIER) cc_final: 0.3392 (tm-30) REVERT: C 1072 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: C 1126 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8182 (m) outliers start: 39 outliers final: 23 residues processed: 67 average time/residue: 0.1465 time to fit residues: 16.8212 Evaluate side-chains 58 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 30 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 62 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 128 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.044363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.029311 restraints weight = 253805.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.030422 restraints weight = 169366.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.030179 restraints weight = 103264.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.030312 restraints weight = 97973.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.030346 restraints weight = 90816.263| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23777 Z= 0.191 Angle : 0.608 12.511 32545 Z= 0.308 Chirality : 0.043 0.258 3943 Planarity : 0.005 0.161 4095 Dihedral : 6.455 85.221 4389 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Rotamer: Outliers : 1.66 % Allowed : 8.26 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.54 (0.15), residues: 2921 helix: 1.97 (0.21), residues: 666 sheet: -0.50 (0.19), residues: 622 loop : -1.34 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.017 0.001 TYR A1067 PHE 0.016 0.001 PHE C 318 TRP 0.009 0.001 TRP B 64 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00416 (23682) covalent geometry : angle 0.58654 (32297) SS BOND : bond 0.00386 ( 37) SS BOND : angle 1.13839 ( 74) hydrogen bonds : bond 0.04081 ( 989) hydrogen bonds : angle 5.86474 ( 2721) link_BETA1-4 : bond 0.00338 ( 12) link_BETA1-4 : angle 1.31930 ( 36) link_NAG-ASN : bond 0.00445 ( 46) link_NAG-ASN : angle 2.32202 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 31 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: A 471 GLU cc_start: 0.9575 (OUTLIER) cc_final: 0.9313 (pp20) REVERT: A 731 MET cc_start: 0.9158 (mtp) cc_final: 0.8957 (ttt) REVERT: A 986 LYS cc_start: 0.9715 (tttt) cc_final: 0.9378 (tptp) REVERT: C 628 GLN cc_start: 0.4304 (OUTLIER) cc_final: 0.3234 (tm-30) REVERT: C 869 MET cc_start: 0.9310 (mtp) cc_final: 0.9056 (mtp) REVERT: C 900 MET cc_start: 0.8737 (mtt) cc_final: 0.8383 (mtt) REVERT: C 1126 CYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8185 (m) outliers start: 39 outliers final: 28 residues processed: 68 average time/residue: 0.1486 time to fit residues: 17.2959 Evaluate side-chains 61 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 29 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 150 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 176 optimal weight: 1.9990 chunk 250 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 165 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 244 optimal weight: 40.0000 overall best weight: 4.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B1048 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.044243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.029310 restraints weight = 251769.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030261 restraints weight = 167326.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030145 restraints weight = 107984.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.030254 restraints weight = 102279.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.030306 restraints weight = 89168.449| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23777 Z= 0.169 Angle : 0.585 12.205 32545 Z= 0.296 Chirality : 0.043 0.251 3943 Planarity : 0.005 0.159 4095 Dihedral : 6.269 77.378 4389 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 1.70 % Allowed : 8.90 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.04 % 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: -0.51 (0.15), residues: 2921 helix: 2.07 (0.21), residues: 668 sheet: -0.66 (0.20), residues: 624 loop : -1.28 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 466 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE C 318 TRP 0.010 0.001 TRP A 633 HIS 0.003 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00369 (23682) covalent geometry : angle 0.56486 (32297) SS BOND : bond 0.00347 ( 37) SS BOND : angle 0.94961 ( 74) hydrogen bonds : bond 0.03955 ( 989) hydrogen bonds : angle 5.74012 ( 2721) link_BETA1-4 : bond 0.00370 ( 12) link_BETA1-4 : angle 1.30028 ( 36) link_NAG-ASN : bond 0.00432 ( 46) link_NAG-ASN : angle 2.23405 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 29 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8842 (m-80) REVERT: A 332 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 471 GLU cc_start: 0.9574 (OUTLIER) cc_final: 0.9306 (pp20) REVERT: A 731 MET cc_start: 0.9116 (mtp) cc_final: 0.8878 (ttt) REVERT: A 986 LYS cc_start: 0.9704 (tttt) cc_final: 0.9375 (tptp) REVERT: A 1029 MET cc_start: 0.8961 (tpt) cc_final: 0.8654 (tpt) REVERT: C 628 GLN cc_start: 0.4206 (OUTLIER) cc_final: 0.3198 (tm-30) REVERT: C 740 MET cc_start: 0.9138 (ttt) cc_final: 0.8909 (ttp) REVERT: C 869 MET cc_start: 0.9223 (mtp) cc_final: 0.8982 (mtp) outliers start: 40 outliers final: 32 residues processed: 67 average time/residue: 0.1399 time to fit residues: 16.3484 Evaluate side-chains 65 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 29 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 950 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 283 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.044240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.029276 restraints weight = 250640.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030222 restraints weight = 171790.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030030 restraints weight = 113182.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.030189 restraints weight = 99240.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.030215 restraints weight = 91604.389| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 23777 Z= 0.170 Angle : 0.581 11.852 32545 Z= 0.293 Chirality : 0.042 0.250 3943 Planarity : 0.005 0.158 4095 Dihedral : 6.159 71.428 4389 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.04 % Rotamer: Outliers : 1.92 % Allowed : 8.73 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.50 (0.15), residues: 2921 helix: 2.11 (0.21), residues: 669 sheet: -0.63 (0.20), residues: 618 loop : -1.30 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.017 0.001 TYR A1067 PHE 0.016 0.001 PHE C 318 TRP 0.020 0.001 TRP A 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00372 (23682) covalent geometry : angle 0.56238 (32297) SS BOND : bond 0.00323 ( 37) SS BOND : angle 0.96381 ( 74) hydrogen bonds : bond 0.03876 ( 989) hydrogen bonds : angle 5.68347 ( 2721) link_BETA1-4 : bond 0.00348 ( 12) link_BETA1-4 : angle 1.29180 ( 36) link_NAG-ASN : bond 0.00414 ( 46) link_NAG-ASN : angle 2.18497 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 30 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: A 118 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9228 (mt) REVERT: A 332 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8610 (tt) REVERT: A 731 MET cc_start: 0.9169 (mtp) cc_final: 0.8960 (ttt) REVERT: A 986 LYS cc_start: 0.9696 (tttt) cc_final: 0.9360 (tptp) REVERT: A 1029 MET cc_start: 0.8924 (tpt) cc_final: 0.8645 (tpt) REVERT: C 628 GLN cc_start: 0.3862 (OUTLIER) cc_final: 0.2931 (tm-30) REVERT: C 869 MET cc_start: 0.9238 (mtp) cc_final: 0.8990 (mtp) REVERT: C 900 MET cc_start: 0.8646 (mtt) cc_final: 0.8303 (mtt) REVERT: C 1126 CYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8174 (m) outliers start: 45 outliers final: 32 residues processed: 73 average time/residue: 0.1456 time to fit residues: 18.5302 Evaluate side-chains 66 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 29 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 132 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 222 optimal weight: 0.0060 chunk 61 optimal weight: 5.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN B 625 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.028044 restraints weight = 252978.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.028781 restraints weight = 157385.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.029196 restraints weight = 119143.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.029518 restraints weight = 100705.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.029626 restraints weight = 90337.591| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23777 Z= 0.143 Angle : 0.566 11.597 32545 Z= 0.286 Chirality : 0.043 0.368 3943 Planarity : 0.005 0.157 4095 Dihedral : 6.018 65.255 4389 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 1.79 % Allowed : 8.94 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.39 (0.16), residues: 2921 helix: 2.17 (0.21), residues: 676 sheet: -0.51 (0.20), residues: 597 loop : -1.26 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE C 318 TRP 0.018 0.001 TRP A 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00314 (23682) covalent geometry : angle 0.54677 (32297) SS BOND : bond 0.00296 ( 37) SS BOND : angle 0.92690 ( 74) hydrogen bonds : bond 0.03752 ( 989) hydrogen bonds : angle 5.57617 ( 2721) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 1.24250 ( 36) link_NAG-ASN : bond 0.00391 ( 46) link_NAG-ASN : angle 2.19982 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 30 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: A 118 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9244 (mt) REVERT: A 332 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 471 GLU cc_start: 0.9555 (OUTLIER) cc_final: 0.9316 (pp20) REVERT: A 986 LYS cc_start: 0.9717 (tttt) cc_final: 0.9391 (tptp) REVERT: A 1029 MET cc_start: 0.9188 (tpt) cc_final: 0.8889 (tpt) REVERT: C 628 GLN cc_start: 0.3966 (OUTLIER) cc_final: 0.3011 (tm-30) REVERT: C 869 MET cc_start: 0.9251 (mtp) cc_final: 0.8955 (mtp) REVERT: C 900 MET cc_start: 0.8724 (mtt) cc_final: 0.8350 (mtt) REVERT: C 1126 CYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8222 (m) outliers start: 42 outliers final: 32 residues processed: 69 average time/residue: 0.1399 time to fit residues: 17.0097 Evaluate side-chains 67 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 29 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 218 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS B 907 ASN B1135 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.044174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029168 restraints weight = 252766.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030242 restraints weight = 169492.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.029973 restraints weight = 105399.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030136 restraints weight = 99747.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.030164 restraints weight = 91574.100| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23777 Z= 0.182 Angle : 0.595 11.453 32545 Z= 0.298 Chirality : 0.043 0.374 3943 Planarity : 0.005 0.156 4095 Dihedral : 6.050 59.221 4389 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 1.70 % Allowed : 9.03 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.44 (0.16), residues: 2921 helix: 2.09 (0.20), residues: 676 sheet: -0.51 (0.20), residues: 612 loop : -1.28 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 634 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE C 318 TRP 0.022 0.002 TRP A 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00397 (23682) covalent geometry : angle 0.57610 (32297) SS BOND : bond 0.00330 ( 37) SS BOND : angle 0.95921 ( 74) hydrogen bonds : bond 0.03870 ( 989) hydrogen bonds : angle 5.64656 ( 2721) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.31227 ( 36) link_NAG-ASN : bond 0.00470 ( 46) link_NAG-ASN : angle 2.23680 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5842 Ramachandran restraints generated. 2921 Oldfield, 0 Emsley, 2921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 30 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: A 118 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9254 (mt) REVERT: A 332 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 471 GLU cc_start: 0.9564 (OUTLIER) cc_final: 0.9318 (pp20) REVERT: A 986 LYS cc_start: 0.9698 (tttt) cc_final: 0.9368 (tptp) REVERT: A 1029 MET cc_start: 0.9019 (tpt) cc_final: 0.8736 (tpt) REVERT: C 628 GLN cc_start: 0.4135 (OUTLIER) cc_final: 0.3176 (tm-30) REVERT: C 869 MET cc_start: 0.9236 (mtp) cc_final: 0.8974 (mtp) REVERT: C 900 MET cc_start: 0.8650 (mtt) cc_final: 0.8285 (mtt) REVERT: C 1126 CYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8179 (m) outliers start: 40 outliers final: 33 residues processed: 68 average time/residue: 0.1426 time to fit residues: 17.0463 Evaluate side-chains 68 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 29 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1083 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 202 optimal weight: 20.0000 chunk 149 optimal weight: 0.1980 chunk 20 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 89 optimal weight: 0.3980 chunk 230 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN B 625 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.044666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.028830 restraints weight = 249745.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.029440 restraints weight = 152505.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.029884 restraints weight = 113944.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030187 restraints weight = 95858.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.030334 restraints weight = 85915.053| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 23777 Z= 0.091 Angle : 0.532 10.953 32545 Z= 0.268 Chirality : 0.042 0.292 3943 Planarity : 0.005 0.155 4095 Dihedral : 5.588 56.310 4389 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 1.19 % Allowed : 9.62 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.17 (0.16), residues: 2921 helix: 2.36 (0.21), residues: 680 sheet: -0.34 (0.20), residues: 597 loop : -1.14 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE C 318 TRP 0.023 0.001 TRP A 633 HIS 0.004 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00199 (23682) covalent geometry : angle 0.51488 (32297) SS BOND : bond 0.00275 ( 37) SS BOND : angle 0.93355 ( 74) hydrogen bonds : bond 0.03396 ( 989) hydrogen bonds : angle 5.28135 ( 2721) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.15001 ( 36) link_NAG-ASN : bond 0.00368 ( 46) link_NAG-ASN : angle 1.98583 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3760.89 seconds wall clock time: 65 minutes 53.08 seconds (3953.08 seconds total)