Starting phenix.real_space_refine on Mon Aug 25 11:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9k_13872/08_2025/7q9k_13872.map" } resolution = 4.5 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= -0.000 sd= 0.026 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 119 5.16 5 C 17312 2.51 5 N 4453 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27225 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7336 Classifications: {'peptide': 943} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7646 Classifications: {'peptide': 979} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 931} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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: "T" 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: "U" 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: "V" 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: 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.96, per 1000 atoms: 0.26 Number of scatterers: 27225 At special positions: 0 Unit cell: (140.22, 141.04, 205, 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 119 16.00 O 5341 8.00 N 4453 7.00 C 17312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.06 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 328 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 600 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 706 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 279 " " NAG C1304 " - " ASN C 328 " " NAG C1305 " - " ASN C 600 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 706 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 714 " " NAG T 1 " - " ASN C 798 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 49 sheets defined 24.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER A 755 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.594A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.771A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.071A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.362A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER B 755 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.595A pdb=" N ASN B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.896A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER C 755 " --> pdb=" O GLN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.597A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.069A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.898A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.602A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.590A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.387A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.560A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.329A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.385A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.893A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.645A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AD8, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.955A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.558A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.492A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3162 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: 7.77 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.35: 8616 1.35 - 1.51: 8406 1.51 - 1.67: 10655 1.67 - 1.83: 153 Bond restraints: 27831 Sorted by residual: bond pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 1.331 1.020 0.311 1.05e-02 9.07e+03 8.78e+02 bond pdb=" C TYR D 104 " pdb=" O TYR D 104 " ideal model delta sigma weight residual 1.233 1.346 -0.113 1.21e-02 6.83e+03 8.76e+01 bond pdb=" C TYR H 104 " pdb=" O TYR H 104 " ideal model delta sigma weight residual 1.233 1.345 -0.112 1.21e-02 6.83e+03 8.56e+01 bond pdb=" N PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" CA TYR H 104 " pdb=" C TYR H 104 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.30e-02 5.92e+03 6.63e+00 ... (remaining 27826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.68: 37854 14.68 - 29.36: 4 29.36 - 44.05: 1 44.05 - 58.73: 0 58.73 - 73.41: 2 Bond angle restraints: 37861 Sorted by residual: angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 122.48 49.07 73.41 1.25e+00 6.40e-01 3.45e+03 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 116.84 46.89 69.95 1.71e+00 3.42e-01 1.67e+03 angle pdb=" O ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 122.59 152.00 -29.41 1.33e+00 5.65e-01 4.89e+02 angle pdb=" CA LYS A 525 " pdb=" C LYS A 525 " pdb=" N LYS A 526 " ideal model delta sigma weight residual 115.78 98.22 17.56 1.35e+00 5.49e-01 1.69e+02 angle pdb=" C LYS A 525 " pdb=" N LYS A 526 " pdb=" CA LYS A 526 " ideal model delta sigma weight residual 121.54 99.60 21.94 1.91e+00 2.74e-01 1.32e+02 ... (remaining 37856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16429 17.85 - 35.71: 604 35.71 - 53.56: 152 53.56 - 71.41: 75 71.41 - 89.27: 20 Dihedral angle restraints: 17280 sinusoidal: 7458 harmonic: 9822 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.36 77.36 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 17277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4022 0.088 - 0.176: 423 0.176 - 0.264: 6 0.264 - 0.352: 7 0.352 - 0.439: 2 Chirality restraints: 4460 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4457 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 525 " -0.075 2.00e-02 2.50e+03 1.62e-01 2.61e+02 pdb=" C LYS A 525 " 0.279 2.00e-02 2.50e+03 pdb=" O LYS A 525 " -0.119 2.00e-02 2.50e+03 pdb=" N LYS A 526 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 328 " 0.125 2.00e-02 2.50e+03 1.33e-01 2.23e+02 pdb=" CG ASN C 328 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 328 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 328 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 328 " -0.016 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C ASN A 328 " -0.157 2.00e-02 2.50e+03 pdb=" O ASN A 328 " 0.071 2.00e-02 2.50e+03 pdb=" N ILE A 329 " 0.102 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 12 2.14 - 2.83: 8211 2.83 - 3.52: 34867 3.52 - 4.21: 65473 4.21 - 4.90: 112251 Nonbonded interactions: 220814 Sorted by model distance: nonbonded pdb=" CB PRO B 518 " pdb=" OH TYR C 200 " model vdw 1.447 3.440 nonbonded pdb=" CB ASN A 328 " pdb=" N ILE A 329 " model vdw 1.680 2.816 nonbonded pdb=" O ASN A 328 " pdb=" CA ILE A 329 " model vdw 1.849 2.776 nonbonded pdb=" CG PRO B 518 " pdb=" CZ TYR C 200 " model vdw 1.927 3.660 nonbonded pdb=" CG PRO B 518 " pdb=" CE1 TYR C 200 " model vdw 1.952 3.740 ... (remaining 220809 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' selection = (chain 'B' and (resid 27 through 439 or resid 499 through 1310)) selection = (chain 'C' and (resid 27 through 439 or resid 499 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.240 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 : 0.005 0.311 27932 Z= 0.286 Angle : 0.896 73.409 38123 Z= 0.543 Chirality : 0.050 0.439 4460 Planarity : 0.005 0.162 4804 Dihedral : 11.189 89.267 10845 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer: Outliers : 0.44 % Allowed : 2.15 % Favored : 97.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: 0.13 (0.14), residues: 3328 helix: 0.67 (0.19), residues: 660 sheet: 0.45 (0.16), residues: 913 loop : -0.25 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 72 TYR 0.018 0.002 TYR D 33 PHE 0.016 0.001 PHE B 55 TRP 0.020 0.002 TRP H 50 HIS 0.005 0.001 HIS C1045 Details of bonding type rmsd covalent geometry : bond 0.00470 (27831) covalent geometry : angle 0.87919 (37861) SS BOND : bond 0.00759 ( 41) SS BOND : angle 1.29438 ( 82) hydrogen bonds : bond 0.17741 ( 1119) hydrogen bonds : angle 7.90886 ( 3162) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 0.71080 ( 45) link_NAG-ASN : bond 0.00378 ( 45) link_NAG-ASN : angle 2.94490 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 378 time to evaluate : 1.070 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: symmetry clash 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: symmetry clash 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: symmetry clash 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 1004 TYR cc_start: 0.8592 (t80) cc_final: 0.8352 (t80) REVERT: A 1064 TYR cc_start: 0.7608 (t80) cc_final: 0.6510 (t80) REVERT: A 1092 PHE cc_start: 0.4942 (m-80) cc_final: 0.4154 (m-80) REVERT: B 37 TYR cc_start: 0.6585 (p90) cc_final: 0.6070 (p90) REVERT: B 49 HIS cc_start: 0.8914 (t70) cc_final: 0.8507 (t70) REVERT: B 711 ILE cc_start: 0.7722 (mt) cc_final: 0.7518 (tt) REVERT: B 745 GLU cc_start: 0.8714 (mp0) cc_final: 0.8161 (tm-30) REVERT: B 760 LEU cc_start: 0.9383 (mt) cc_final: 0.9180 (mt) REVERT: B 767 ILE cc_start: 0.9390 (mt) cc_final: 0.8802 (pt) REVERT: C 55 PHE cc_start: 0.9124 (m-80) cc_final: 0.8214 (m-80) REVERT: C 744 THR cc_start: 0.9401 (m) cc_final: 0.9091 (p) REVERT: C 1106 PHE cc_start: 0.9221 (t80) cc_final: 0.8990 (t80) REVERT: L 4 MET cc_start: 0.8379 (mmm) cc_final: 0.7980 (mmm) outliers start: 13 outliers final: 5 residues processed: 389 average time/residue: 0.2178 time to fit residues: 128.3557 Evaluate side-chains 203 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 50.0000 overall best weight: 6.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A 869 GLN A 898 GLN A 999 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN B 801 GLN B 869 GLN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 999 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN C 748 ASN C 869 GLN C 898 GLN C1051 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN H 117 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.081336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.063144 restraints weight = 295389.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.062307 restraints weight = 203105.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.063303 restraints weight = 160308.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.063483 restraints weight = 111703.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.063462 restraints weight = 99921.678| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 27932 Z= 0.263 Angle : 0.792 14.675 38123 Z= 0.409 Chirality : 0.049 0.298 4460 Planarity : 0.005 0.091 4804 Dihedral : 6.570 51.336 4879 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 0.14 % Allowed : 1.53 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: 0.15 (0.14), residues: 3328 helix: 0.90 (0.20), residues: 661 sheet: 0.36 (0.16), residues: 898 loop : -0.28 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 902 TYR 0.036 0.002 TYR A 200 PHE 0.031 0.002 PHE A 756 TRP 0.010 0.002 TRP L 32 HIS 0.009 0.002 HIS B1061 Details of bonding type rmsd covalent geometry : bond 0.00532 (27831) covalent geometry : angle 0.77524 (37861) SS BOND : bond 0.00860 ( 41) SS BOND : angle 1.28683 ( 82) hydrogen bonds : bond 0.04990 ( 1119) hydrogen bonds : angle 6.56230 ( 3162) link_BETA1-4 : bond 0.00816 ( 15) link_BETA1-4 : angle 1.08609 ( 45) link_NAG-ASN : bond 0.01015 ( 45) link_NAG-ASN : angle 2.71384 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 238 time to evaluate : 1.105 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 737 MET cc_start: 0.9575 (tpt) cc_final: 0.9298 (tpp) REVERT: A 866 MET cc_start: 0.9420 (mtt) cc_final: 0.9198 (mtt) REVERT: A 897 MET cc_start: 0.7316 (mmt) cc_final: 0.7099 (mmt) REVERT: A 976 ASP cc_start: 0.9651 (m-30) cc_final: 0.9445 (t0) REVERT: A 993 LEU cc_start: 0.9623 (pp) cc_final: 0.9402 (mm) REVERT: A 1064 TYR cc_start: 0.8297 (t80) cc_final: 0.7745 (t80) REVERT: B 562 PHE cc_start: 0.8637 (m-10) cc_final: 0.8383 (m-80) REVERT: B 745 GLU cc_start: 0.8899 (mp0) cc_final: 0.8533 (tt0) REVERT: B 858 LEU cc_start: 0.9460 (tp) cc_final: 0.9229 (tp) REVERT: B 866 MET cc_start: 0.9599 (mtm) cc_final: 0.9288 (ptp) REVERT: B 924 PHE cc_start: 0.9358 (t80) cc_final: 0.9127 (t80) REVERT: B 982 ASP cc_start: 0.9042 (m-30) cc_final: 0.8671 (p0) REVERT: B 1004 TYR cc_start: 0.9651 (t80) cc_final: 0.9391 (t80) REVERT: B 1007 GLN cc_start: 0.9452 (OUTLIER) cc_final: 0.8988 (pp30) REVERT: C 331 ASN cc_start: 0.9007 (t0) cc_final: 0.8698 (p0) REVERT: C 753 TYR cc_start: 0.8431 (m-10) cc_final: 0.8066 (m-80) REVERT: C 924 PHE cc_start: 0.9348 (t80) cc_final: 0.9046 (t80) REVERT: C 982 ASP cc_start: 0.8982 (p0) cc_final: 0.8681 (p0) REVERT: C 1047 MET cc_start: 0.9402 (tpt) cc_final: 0.9080 (tpt) REVERT: H 81 MET cc_start: 0.3637 (mmm) cc_final: 0.2663 (mmm) outliers start: 4 outliers final: 1 residues processed: 242 average time/residue: 0.2081 time to fit residues: 78.4645 Evaluate side-chains 154 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 198 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 323 optimal weight: 0.0870 chunk 318 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 316 optimal weight: 40.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 196 ASN ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 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 = 0.4055 r_free = 0.4055 target = 0.079502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.058356 restraints weight = 298509.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.057093 restraints weight = 197571.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.057830 restraints weight = 140104.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.058320 restraints weight = 110747.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.058399 restraints weight = 91942.755| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 27932 Z= 0.187 Angle : 0.646 21.564 38123 Z= 0.332 Chirality : 0.047 0.709 4460 Planarity : 0.005 0.141 4804 Dihedral : 5.985 55.853 4879 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: 0.22 (0.14), residues: 3328 helix: 1.06 (0.20), residues: 657 sheet: 0.31 (0.16), residues: 887 loop : -0.20 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 237 TYR 0.026 0.002 TYR A 870 PHE 0.027 0.002 PHE A 756 TRP 0.037 0.002 TRP D 36 HIS 0.009 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00378 (27831) covalent geometry : angle 0.62178 (37861) SS BOND : bond 0.00418 ( 41) SS BOND : angle 1.16168 ( 82) hydrogen bonds : bond 0.04386 ( 1119) hydrogen bonds : angle 6.27865 ( 3162) link_BETA1-4 : bond 0.00522 ( 15) link_BETA1-4 : angle 1.38311 ( 45) link_NAG-ASN : bond 0.00460 ( 45) link_NAG-ASN : angle 2.82511 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.126 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9613 (tpt) cc_final: 0.9347 (tpp) REVERT: A 866 MET cc_start: 0.9488 (mtt) cc_final: 0.9206 (mpp) REVERT: A 976 ASP cc_start: 0.9650 (m-30) cc_final: 0.9449 (t0) REVERT: A 1064 TYR cc_start: 0.8249 (t80) cc_final: 0.7899 (t80) REVERT: B 37 TYR cc_start: 0.8409 (p90) cc_final: 0.7936 (p90) REVERT: B 562 PHE cc_start: 0.8704 (m-10) cc_final: 0.8467 (m-80) REVERT: B 767 ILE cc_start: 0.9471 (mt) cc_final: 0.9251 (mt) REVERT: B 861 LEU cc_start: 0.9077 (tp) cc_final: 0.8850 (mm) REVERT: B 924 PHE cc_start: 0.9283 (t80) cc_final: 0.9021 (t80) REVERT: B 961 LYS cc_start: 0.9610 (ptpp) cc_final: 0.9382 (pttp) REVERT: B 982 ASP cc_start: 0.9050 (m-30) cc_final: 0.8517 (p0) REVERT: B 1004 TYR cc_start: 0.9157 (t80) cc_final: 0.8918 (t80) REVERT: B 1007 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8900 (pp30) REVERT: B 1049 PHE cc_start: 0.8807 (m-80) cc_final: 0.8566 (m-80) REVERT: B 1107 TYR cc_start: 0.8723 (t80) cc_final: 0.8461 (t80) REVERT: B 1110 GLN cc_start: 0.8582 (pt0) cc_final: 0.8342 (pm20) REVERT: C 40 ASP cc_start: 0.8814 (t0) cc_final: 0.8545 (t70) REVERT: C 331 ASN cc_start: 0.9166 (t0) cc_final: 0.8873 (p0) REVERT: C 753 TYR cc_start: 0.8582 (m-10) cc_final: 0.8119 (m-80) REVERT: H 81 MET cc_start: 0.3322 (mmm) cc_final: 0.3076 (mmm) REVERT: D 70 MET cc_start: 0.8553 (ttt) cc_final: 0.8280 (ttt) REVERT: D 81 MET cc_start: 0.4289 (mtp) cc_final: 0.1840 (mmm) outliers start: 2 outliers final: 0 residues processed: 220 average time/residue: 0.1990 time to fit residues: 69.0581 Evaluate side-chains 154 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 118 optimal weight: 0.0970 chunk 302 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN B 87 ASN B 484 ASN B 801 GLN B 821 ASN B1116 ASN C1002 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.076258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.053541 restraints weight = 304680.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.052632 restraints weight = 198217.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.053321 restraints weight = 142120.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.053515 restraints weight = 114424.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.053520 restraints weight = 101259.853| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 27932 Z= 0.208 Angle : 0.653 13.209 38123 Z= 0.338 Chirality : 0.046 0.651 4460 Planarity : 0.004 0.057 4804 Dihedral : 5.724 52.913 4879 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.05 (0.14), residues: 3328 helix: 0.67 (0.20), residues: 662 sheet: 0.13 (0.17), residues: 901 loop : -0.30 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 61 TYR 0.019 0.002 TYR B1064 PHE 0.027 0.002 PHE B 715 TRP 0.010 0.001 TRP D 36 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00422 (27831) covalent geometry : angle 0.63644 (37861) SS BOND : bond 0.00598 ( 41) SS BOND : angle 1.03957 ( 82) hydrogen bonds : bond 0.04316 ( 1119) hydrogen bonds : angle 6.33783 ( 3162) link_BETA1-4 : bond 0.00499 ( 15) link_BETA1-4 : angle 1.33154 ( 45) link_NAG-ASN : bond 0.00475 ( 45) link_NAG-ASN : angle 2.36161 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 1.111 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9645 (tpt) cc_final: 0.9334 (tpp) REVERT: A 866 MET cc_start: 0.9354 (mtt) cc_final: 0.9011 (mtp) REVERT: A 1064 TYR cc_start: 0.8521 (t80) cc_final: 0.8167 (t80) REVERT: B 37 TYR cc_start: 0.8645 (p90) cc_final: 0.7263 (p90) REVERT: B 562 PHE cc_start: 0.8660 (m-10) cc_final: 0.8405 (m-80) REVERT: B 711 ILE cc_start: 0.9096 (mt) cc_final: 0.8827 (mp) REVERT: B 772 ASP cc_start: 0.9338 (t0) cc_final: 0.8771 (p0) REVERT: B 866 MET cc_start: 0.8728 (ppp) cc_final: 0.8462 (ppp) REVERT: B 961 LYS cc_start: 0.9627 (ptpp) cc_final: 0.9403 (pttp) REVERT: B 982 ASP cc_start: 0.9146 (m-30) cc_final: 0.8595 (p0) REVERT: B 1099 TRP cc_start: 0.8606 (m100) cc_final: 0.8231 (m100) REVERT: B 1107 TYR cc_start: 0.8674 (t80) cc_final: 0.8420 (t80) REVERT: C 40 ASP cc_start: 0.8901 (t0) cc_final: 0.8645 (t70) REVERT: C 117 LEU cc_start: 0.9130 (tp) cc_final: 0.8868 (tp) REVERT: C 331 ASN cc_start: 0.9253 (t0) cc_final: 0.8971 (p0) REVERT: C 753 TYR cc_start: 0.8721 (m-10) cc_final: 0.8271 (m-80) REVERT: C 759 GLN cc_start: 0.9418 (pt0) cc_final: 0.9212 (pt0) REVERT: C 1047 MET cc_start: 0.9601 (tpt) cc_final: 0.9316 (tpt) REVERT: H 81 MET cc_start: 0.3342 (mmm) cc_final: 0.3074 (tpp) REVERT: D 81 MET cc_start: 0.3151 (mtp) cc_final: 0.2851 (mtp) outliers start: 3 outliers final: 0 residues processed: 197 average time/residue: 0.2006 time to fit residues: 62.4664 Evaluate side-chains 137 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 126 optimal weight: 30.0000 chunk 216 optimal weight: 7.9990 chunk 308 optimal weight: 50.0000 chunk 178 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 327 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 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 761 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 904 ASN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 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 = 0.3943 r_free = 0.3943 target = 0.074582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.055139 restraints weight = 306528.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.054755 restraints weight = 214032.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.055324 restraints weight = 158757.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.055645 restraints weight = 117344.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.055624 restraints weight = 86081.365| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 27932 Z= 0.204 Angle : 0.638 13.539 38123 Z= 0.333 Chirality : 0.045 0.490 4460 Planarity : 0.004 0.067 4804 Dihedral : 5.722 54.405 4879 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.11 (0.14), residues: 3328 helix: 0.73 (0.20), residues: 661 sheet: 0.12 (0.17), residues: 883 loop : -0.42 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 762 TYR 0.023 0.002 TYR B 37 PHE 0.017 0.002 PHE C 315 TRP 0.010 0.001 TRP H 50 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00413 (27831) covalent geometry : angle 0.62045 (37861) SS BOND : bond 0.01060 ( 41) SS BOND : angle 1.43295 ( 82) hydrogen bonds : bond 0.04287 ( 1119) hydrogen bonds : angle 6.36922 ( 3162) link_BETA1-4 : bond 0.00437 ( 15) link_BETA1-4 : angle 1.32531 ( 45) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.30639 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.108 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.8302 (m-10) cc_final: 0.7738 (m-80) REVERT: A 737 MET cc_start: 0.9591 (tpt) cc_final: 0.9325 (tpp) REVERT: A 866 MET cc_start: 0.9290 (mtt) cc_final: 0.8916 (mtp) REVERT: A 1064 TYR cc_start: 0.8567 (t80) cc_final: 0.8146 (t80) REVERT: A 1092 PHE cc_start: 0.7068 (m-10) cc_final: 0.6124 (m-80) REVERT: B 37 TYR cc_start: 0.8689 (p90) cc_final: 0.8480 (p90) REVERT: B 562 PHE cc_start: 0.8491 (m-10) cc_final: 0.8207 (m-80) REVERT: B 711 ILE cc_start: 0.9217 (mt) cc_final: 0.8913 (mp) REVERT: B 961 LYS cc_start: 0.9621 (ptpp) cc_final: 0.9382 (pttp) REVERT: B 982 ASP cc_start: 0.9122 (m-30) cc_final: 0.8555 (p0) REVERT: B 1099 TRP cc_start: 0.8839 (m100) cc_final: 0.8420 (m100) REVERT: C 40 ASP cc_start: 0.8955 (t0) cc_final: 0.8684 (t70) REVERT: C 331 ASN cc_start: 0.9248 (t0) cc_final: 0.8954 (p0) REVERT: C 568 ASP cc_start: 0.8892 (t0) cc_final: 0.8689 (t0) REVERT: C 759 GLN cc_start: 0.9435 (pt0) cc_final: 0.9192 (pt0) REVERT: D 81 MET cc_start: 0.3490 (mtp) cc_final: 0.2682 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2012 time to fit residues: 59.3502 Evaluate side-chains 137 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 128 optimal weight: 40.0000 chunk 315 optimal weight: 50.0000 chunk 324 optimal weight: 50.0000 chunk 98 optimal weight: 0.3980 chunk 277 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 297 optimal weight: 40.0000 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 ASN B1132 ASN C 385 ASN ** C 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.072081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.049110 restraints weight = 311049.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.048015 restraints weight = 203877.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.048529 restraints weight = 147107.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.048727 restraints weight = 119051.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.049059 restraints weight = 107956.001| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 27932 Z= 0.237 Angle : 0.716 15.860 38123 Z= 0.366 Chirality : 0.047 0.493 4460 Planarity : 0.005 0.074 4804 Dihedral : 6.128 59.875 4879 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.48 (0.14), residues: 3328 helix: 0.35 (0.20), residues: 655 sheet: -0.01 (0.17), residues: 865 loop : -0.66 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 762 TYR 0.026 0.002 TYR B1064 PHE 0.028 0.002 PHE A1086 TRP 0.011 0.001 TRP C 64 HIS 0.007 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00476 (27831) covalent geometry : angle 0.69406 (37861) SS BOND : bond 0.00516 ( 41) SS BOND : angle 1.34057 ( 82) hydrogen bonds : bond 0.04605 ( 1119) hydrogen bonds : angle 6.63819 ( 3162) link_BETA1-4 : bond 0.00422 ( 15) link_BETA1-4 : angle 1.67969 ( 45) link_NAG-ASN : bond 0.00640 ( 45) link_NAG-ASN : angle 2.74966 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.954 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.8338 (m) cc_final: 0.8102 (t) REVERT: A 561 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8803 (tp-100) REVERT: A 737 MET cc_start: 0.9533 (tpt) cc_final: 0.9316 (tpp) REVERT: B 711 ILE cc_start: 0.9246 (mt) cc_final: 0.9026 (mp) REVERT: B 738 TYR cc_start: 0.8411 (t80) cc_final: 0.8145 (t80) REVERT: B 772 ASP cc_start: 0.9346 (t0) cc_final: 0.8808 (p0) REVERT: B 961 LYS cc_start: 0.9598 (ptpp) cc_final: 0.9369 (pttp) REVERT: B 982 ASP cc_start: 0.9088 (m-30) cc_final: 0.8444 (p0) REVERT: B 1092 PHE cc_start: 0.7425 (m-10) cc_final: 0.5608 (m-80) REVERT: B 1099 TRP cc_start: 0.9036 (m100) cc_final: 0.8564 (m100) REVERT: B 1107 TYR cc_start: 0.8509 (t80) cc_final: 0.8189 (t80) REVERT: C 331 ASN cc_start: 0.9299 (t0) cc_final: 0.9001 (p0) REVERT: C 568 ASP cc_start: 0.8910 (t0) cc_final: 0.8701 (t0) REVERT: C 711 ILE cc_start: 0.8082 (mt) cc_final: 0.7672 (mp) REVERT: C 753 TYR cc_start: 0.8806 (m-80) cc_final: 0.8375 (m-80) REVERT: C 759 GLN cc_start: 0.9405 (pt0) cc_final: 0.9176 (pt0) REVERT: C 919 LEU cc_start: 0.9232 (tp) cc_final: 0.8851 (pp) REVERT: C 1016 ARG cc_start: 0.9307 (tpt-90) cc_final: 0.9098 (tpp80) REVERT: C 1047 MET cc_start: 0.9618 (tpt) cc_final: 0.9103 (tpt) REVERT: C 1059 PHE cc_start: 0.9222 (m-80) cc_final: 0.8996 (m-10) REVERT: H 81 MET cc_start: 0.3816 (mmm) cc_final: 0.3612 (mmt) REVERT: D 81 MET cc_start: 0.3366 (mtp) cc_final: 0.3096 (mtp) outliers start: 3 outliers final: 0 residues processed: 168 average time/residue: 0.1865 time to fit residues: 49.6955 Evaluate side-chains 128 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 299 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 196 optimal weight: 0.0070 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 821 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 311 GLN B 610 GLN C 652 HIS C 869 GLN C 904 ASN ** C 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN H 59 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.073307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.054303 restraints weight = 305234.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.053193 restraints weight = 216438.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.053917 restraints weight = 167085.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.054220 restraints weight = 115674.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.054206 restraints weight = 90293.297| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27932 Z= 0.159 Angle : 0.618 12.026 38123 Z= 0.318 Chirality : 0.045 0.449 4460 Planarity : 0.004 0.058 4804 Dihedral : 5.910 59.421 4879 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.34 (0.14), residues: 3328 helix: 0.69 (0.20), residues: 666 sheet: -0.02 (0.18), residues: 845 loop : -0.62 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 762 TYR 0.021 0.001 TYR A1004 PHE 0.030 0.002 PHE B1039 TRP 0.014 0.001 TRP A 883 HIS 0.010 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00324 (27831) covalent geometry : angle 0.59865 (37861) SS BOND : bond 0.00319 ( 41) SS BOND : angle 1.13329 ( 82) hydrogen bonds : bond 0.04036 ( 1119) hydrogen bonds : angle 6.36260 ( 3162) link_BETA1-4 : bond 0.00508 ( 15) link_BETA1-4 : angle 1.35905 ( 45) link_NAG-ASN : bond 0.00517 ( 45) link_NAG-ASN : angle 2.41458 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.258 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8676 (tp-100) REVERT: A 737 MET cc_start: 0.9493 (tpt) cc_final: 0.9287 (tpp) REVERT: A 1092 PHE cc_start: 0.7320 (m-10) cc_final: 0.6515 (m-80) REVERT: B 51 THR cc_start: 0.9755 (t) cc_final: 0.9279 (t) REVERT: B 982 ASP cc_start: 0.9105 (m-30) cc_final: 0.8438 (p0) REVERT: B 1092 PHE cc_start: 0.7316 (m-10) cc_final: 0.6083 (m-80) REVERT: C 331 ASN cc_start: 0.9325 (t0) cc_final: 0.9023 (p0) REVERT: C 568 ASP cc_start: 0.8921 (t0) cc_final: 0.8685 (t0) REVERT: C 866 MET cc_start: 0.9468 (mmp) cc_final: 0.9261 (mmm) REVERT: C 1047 MET cc_start: 0.9620 (tpt) cc_final: 0.9128 (tpt) REVERT: D 81 MET cc_start: 0.3548 (mtp) cc_final: 0.3136 (mtp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1904 time to fit residues: 47.6417 Evaluate side-chains 119 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 172 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 288 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 445 ASN L 27 GLN D 59 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.072752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.052799 restraints weight = 310087.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.051985 restraints weight = 216530.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.052339 restraints weight = 170049.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.052879 restraints weight = 123024.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.052808 restraints weight = 92960.228| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.7335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27932 Z= 0.162 Angle : 0.616 12.594 38123 Z= 0.316 Chirality : 0.045 0.428 4460 Planarity : 0.004 0.058 4804 Dihedral : 5.802 54.204 4879 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.29 (0.15), residues: 3328 helix: 0.84 (0.20), residues: 664 sheet: 0.02 (0.17), residues: 855 loop : -0.64 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 992 TYR 0.025 0.001 TYR A1004 PHE 0.032 0.002 PHE B 967 TRP 0.014 0.001 TRP A 883 HIS 0.021 0.002 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00337 (27831) covalent geometry : angle 0.59216 (37861) SS BOND : bond 0.00374 ( 41) SS BOND : angle 1.23522 ( 82) hydrogen bonds : bond 0.03980 ( 1119) hydrogen bonds : angle 6.23508 ( 3162) link_BETA1-4 : bond 0.00410 ( 15) link_BETA1-4 : angle 1.37739 ( 45) link_NAG-ASN : bond 0.00522 ( 45) link_NAG-ASN : angle 2.72042 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.963 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9111 (mp) cc_final: 0.8642 (tp) REVERT: A 561 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8666 (tp-100) REVERT: A 728 MET cc_start: 0.9117 (ppp) cc_final: 0.8899 (ppp) REVERT: A 1064 TYR cc_start: 0.8703 (t80) cc_final: 0.8500 (t80) REVERT: A 1092 PHE cc_start: 0.7235 (m-10) cc_final: 0.6480 (m-80) REVERT: B 51 THR cc_start: 0.9577 (t) cc_final: 0.9325 (t) REVERT: B 772 ASP cc_start: 0.9349 (t0) cc_final: 0.8831 (p0) REVERT: B 982 ASP cc_start: 0.9090 (m-30) cc_final: 0.8432 (p0) REVERT: B 1092 PHE cc_start: 0.7056 (m-80) cc_final: 0.5465 (m-80) REVERT: C 331 ASN cc_start: 0.9297 (t0) cc_final: 0.8996 (p0) REVERT: C 568 ASP cc_start: 0.8942 (t0) cc_final: 0.8708 (t0) REVERT: C 866 MET cc_start: 0.9473 (mmp) cc_final: 0.9268 (mmm) REVERT: C 919 LEU cc_start: 0.9132 (tp) cc_final: 0.8777 (pp) REVERT: C 1047 MET cc_start: 0.9540 (tpt) cc_final: 0.9075 (tpt) REVERT: D 81 MET cc_start: 0.3361 (mtp) cc_final: 0.2421 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1936 time to fit residues: 47.4679 Evaluate side-chains 123 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 187 optimal weight: 20.0000 chunk 273 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 152 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 100 optimal weight: 40.0000 chunk 249 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN H 39 GLN L 38 GLN ** E 89 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 = 0.3875 r_free = 0.3875 target = 0.071928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.052243 restraints weight = 311361.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.051619 restraints weight = 217496.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.052054 restraints weight = 156833.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.052234 restraints weight = 120078.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.051911 restraints weight = 104195.432| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27932 Z= 0.173 Angle : 0.632 10.919 38123 Z= 0.324 Chirality : 0.045 0.409 4460 Planarity : 0.004 0.059 4804 Dihedral : 5.780 55.340 4879 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.31 (0.15), residues: 3328 helix: 0.77 (0.20), residues: 671 sheet: 0.02 (0.18), residues: 844 loop : -0.64 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 24 TYR 0.027 0.002 TYR B1064 PHE 0.025 0.002 PHE C1039 TRP 0.023 0.002 TRP C1099 HIS 0.017 0.002 HIS B1045 Details of bonding type rmsd covalent geometry : bond 0.00353 (27831) covalent geometry : angle 0.60725 (37861) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.72154 ( 82) hydrogen bonds : bond 0.03961 ( 1119) hydrogen bonds : angle 6.22557 ( 3162) link_BETA1-4 : bond 0.00396 ( 15) link_BETA1-4 : angle 1.37211 ( 45) link_NAG-ASN : bond 0.00584 ( 45) link_NAG-ASN : angle 2.62829 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.122 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.7623 (p90) cc_final: 0.7352 (p90) REVERT: A 561 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8764 (tp-100) REVERT: A 728 MET cc_start: 0.9128 (ppp) cc_final: 0.8866 (ppp) REVERT: A 866 MET cc_start: 0.9353 (mtt) cc_final: 0.9046 (mtt) REVERT: A 1064 TYR cc_start: 0.8703 (t80) cc_final: 0.8481 (t80) REVERT: A 1092 PHE cc_start: 0.7177 (m-10) cc_final: 0.6456 (m-80) REVERT: B 772 ASP cc_start: 0.9356 (t0) cc_final: 0.8820 (p0) REVERT: B 982 ASP cc_start: 0.9043 (m-30) cc_final: 0.8386 (p0) REVERT: B 1049 PHE cc_start: 0.8989 (m-80) cc_final: 0.8726 (m-80) REVERT: B 1064 TYR cc_start: 0.8237 (t80) cc_final: 0.7828 (t80) REVERT: B 1092 PHE cc_start: 0.7038 (m-80) cc_final: 0.6181 (m-80) REVERT: C 568 ASP cc_start: 0.8929 (t0) cc_final: 0.8700 (t0) REVERT: C 694 MET cc_start: 0.8300 (tmm) cc_final: 0.8055 (tmm) REVERT: C 919 LEU cc_start: 0.9177 (tp) cc_final: 0.8805 (pp) REVERT: C 989 GLN cc_start: 0.9209 (mp10) cc_final: 0.8995 (mp10) REVERT: C 1047 MET cc_start: 0.9587 (tpt) cc_final: 0.9087 (tpt) REVERT: D 81 MET cc_start: 0.4403 (mtp) cc_final: 0.2492 (mtp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1935 time to fit residues: 46.9860 Evaluate side-chains 120 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 184 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 225 optimal weight: 50.0000 chunk 130 optimal weight: 50.0000 chunk 82 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 218 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN ** E 89 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 = 0.3885 r_free = 0.3885 target = 0.072215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.049771 restraints weight = 310122.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.049509 restraints weight = 198788.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.049566 restraints weight = 143849.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.049928 restraints weight = 113732.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.050201 restraints weight = 96720.203| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27932 Z= 0.150 Angle : 0.613 10.439 38123 Z= 0.314 Chirality : 0.045 0.394 4460 Planarity : 0.004 0.058 4804 Dihedral : 5.680 55.160 4879 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.28 (0.15), residues: 3328 helix: 0.87 (0.20), residues: 670 sheet: 0.03 (0.17), residues: 856 loop : -0.66 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 992 TYR 0.023 0.001 TYR B1064 PHE 0.028 0.002 PHE C1100 TRP 0.012 0.001 TRP C1099 HIS 0.015 0.002 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00309 (27831) covalent geometry : angle 0.59098 (37861) SS BOND : bond 0.00329 ( 41) SS BOND : angle 1.56388 ( 82) hydrogen bonds : bond 0.03889 ( 1119) hydrogen bonds : angle 6.13073 ( 3162) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.28282 ( 45) link_NAG-ASN : bond 0.00473 ( 45) link_NAG-ASN : angle 2.45631 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.111 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9185 (mp) cc_final: 0.8631 (tp) REVERT: A 559 PHE cc_start: 0.7819 (p90) cc_final: 0.7518 (p90) REVERT: A 561 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8736 (tp-100) REVERT: A 728 MET cc_start: 0.9195 (ppp) cc_final: 0.8901 (ppp) REVERT: A 866 MET cc_start: 0.9303 (mtt) cc_final: 0.8882 (mtp) REVERT: A 1064 TYR cc_start: 0.8787 (t80) cc_final: 0.8569 (t80) REVERT: A 1092 PHE cc_start: 0.7426 (m-10) cc_final: 0.6726 (m-80) REVERT: B 982 ASP cc_start: 0.9065 (m-30) cc_final: 0.8408 (p0) REVERT: B 1064 TYR cc_start: 0.8264 (t80) cc_final: 0.7821 (t80) REVERT: B 1092 PHE cc_start: 0.7235 (m-80) cc_final: 0.6411 (m-80) REVERT: C 568 ASP cc_start: 0.8956 (t0) cc_final: 0.8738 (t0) REVERT: C 919 LEU cc_start: 0.9151 (tp) cc_final: 0.8788 (pp) REVERT: C 1047 MET cc_start: 0.9551 (tpt) cc_final: 0.9096 (tpt) REVERT: D 81 MET cc_start: 0.3778 (mtp) cc_final: 0.3336 (mtp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2095 time to fit residues: 49.6134 Evaluate side-chains 120 residues out of total 2940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 304 optimal weight: 10.0000 chunk 262 optimal weight: 0.0170 chunk 239 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 97 optimal weight: 0.0170 chunk 177 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 overall best weight: 3.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 HIS A1002 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN H 3 GLN H 59 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.071863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.048764 restraints weight = 306748.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.047770 restraints weight = 197084.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.048277 restraints weight = 139817.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.048717 restraints weight = 111411.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.048718 restraints weight = 96009.640| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.8284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27932 Z= 0.151 Angle : 0.606 10.222 38123 Z= 0.311 Chirality : 0.045 0.387 4460 Planarity : 0.004 0.058 4804 Dihedral : 5.688 58.538 4879 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 aren not related in a simple way. whole: -0.27 (0.15), residues: 3328 helix: 0.93 (0.20), residues: 670 sheet: 0.10 (0.17), residues: 846 loop : -0.70 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.025 0.001 TYR B1064 PHE 0.032 0.002 PHE C 133 TRP 0.016 0.001 TRP B1099 HIS 0.014 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00313 (27831) covalent geometry : angle 0.58426 (37861) SS BOND : bond 0.00321 ( 41) SS BOND : angle 1.51171 ( 82) hydrogen bonds : bond 0.03806 ( 1119) hydrogen bonds : angle 6.07478 ( 3162) link_BETA1-4 : bond 0.00464 ( 15) link_BETA1-4 : angle 1.31340 ( 45) link_NAG-ASN : bond 0.00463 ( 45) link_NAG-ASN : angle 2.41954 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7682.04 seconds wall clock time: 132 minutes 33.99 seconds (7953.99 seconds total)