Starting phenix.real_space_refine on Mon Aug 25 11:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qur_14152/08_2025/7qur_14152.map" } resolution = 2.27 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= 0.006 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 9 10.91 5 S 120 5.16 5 C 17094 2.51 5 N 4386 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 27174 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "B" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "C" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 221 Unusual residues: {'EIC': 1, 'GE9': 1, 'NAG': 12, 'SIA': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 505 " occ=0.50 residue: pdb=" N ATYR B 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 505 " occ=0.50 residue: pdb=" N ATYR C 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 505 " occ=0.50 Time building chain proxies: 10.49, per 1000 atoms: 0.39 Number of scatterers: 27174 At special positions: 0 Unit cell: (141.04, 156.62, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 9 52.95 S 120 16.00 O 5565 8.00 N 4386 7.00 C 17094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 149 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 165 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 165 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 25.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.963A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.471A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.552A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.606A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.001A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.552A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.963A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.471A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.553A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.606A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.001A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.551A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.964A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.472A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.553A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 843 through 848 removed outlier: 3.607A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.002A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.551A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.017A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.927A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 76 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.927A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.439A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.804A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.184A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.050A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1121 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.439A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 12.805A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.389A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.050A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 76 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.438A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.804A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.919A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.049A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.203A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1121 through 1122 1118 hydrogen bonds defined for protein. 3009 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: 7.32 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 8523 1.35 - 1.54: 18366 1.54 - 1.73: 444 1.73 - 1.92: 150 1.92 - 2.11: 9 Bond restraints: 27492 Sorted by residual: bond pdb=" C10 SIA C1315 " pdb=" N5 SIA C1315 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C10 SIA B1314 " pdb=" N5 SIA B1314 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" C10 SIA A1314 " pdb=" N5 SIA A1314 " ideal model delta sigma weight residual 1.358 1.510 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C07 GE9 A1313 " pdb=" N01 GE9 A1313 " ideal model delta sigma weight residual 1.336 1.451 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C07 GE9 B1313 " pdb=" N01 GE9 B1313 " ideal model delta sigma weight residual 1.336 1.451 -0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 27487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 37339 5.04 - 10.09: 62 10.09 - 15.13: 0 15.13 - 20.17: 3 20.17 - 25.21: 3 Bond angle restraints: 37407 Sorted by residual: angle pdb=" C11 EIC A1315 " pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " ideal model delta sigma weight residual 127.32 152.53 -25.21 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C11 EIC B1315 " pdb=" C10 EIC B1315 " pdb=" C9 EIC B1315 " ideal model delta sigma weight residual 127.32 152.53 -25.21 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C11 EIC C1301 " pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 127.32 152.50 -25.18 3.00e+00 1.11e-01 7.04e+01 angle pdb=" C10 EIC A1315 " pdb=" C9 EIC A1315 " pdb=" C8 EIC A1315 " ideal model delta sigma weight residual 127.75 111.99 15.76 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C10 EIC B1315 " pdb=" C9 EIC B1315 " pdb=" C8 EIC B1315 " ideal model delta sigma weight residual 127.75 112.00 15.75 3.00e+00 1.11e-01 2.75e+01 ... (remaining 37402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 15321 17.75 - 35.49: 1377 35.49 - 53.24: 393 53.24 - 70.99: 126 70.99 - 88.74: 42 Dihedral angle restraints: 17259 sinusoidal: 7629 harmonic: 9630 Sorted by residual: dihedral pdb=" CA VAL B 615 " pdb=" C VAL B 615 " pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA VAL A 615 " pdb=" C VAL A 615 " pdb=" N ASN A 616 " pdb=" CA ASN A 616 " ideal model delta harmonic sigma weight residual 180.00 147.88 32.12 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA VAL C 615 " pdb=" C VAL C 615 " pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 17256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4407 0.149 - 0.298: 3 0.298 - 0.447: 3 0.447 - 0.596: 0 0.596 - 0.745: 3 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 ... (remaining 4413 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO C 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO B 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 208 " -0.049 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO A 209 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 209 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 209 " -0.041 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.71: 788 2.71 - 3.27: 26566 3.27 - 3.83: 49755 3.83 - 4.40: 63814 4.40 - 4.96: 104501 Nonbonded interactions: 245424 Sorted by model distance: nonbonded pdb=" OG1 THR C 645 " pdb=" O ARG C 646 " model vdw 2.145 3.040 nonbonded pdb=" OG1 THR A 645 " pdb=" O ARG A 646 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR B 645 " pdb=" O ARG B 646 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR A 676 " pdb=" OE1 GLN A 690 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 676 " pdb=" OE1 GLN C 690 " model vdw 2.202 3.040 ... (remaining 245419 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: 0.07 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) selection = (chain 'C' and (resid 14 through 504 or resid 506 through 877 or resid 879 throu \ gh 1139 or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.940 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 0.152 27600 Z= 0.240 Angle : 0.737 25.213 37689 Z= 0.326 Chirality : 0.049 0.745 4416 Planarity : 0.004 0.075 4752 Dihedral : 15.739 88.735 10959 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.01 % Allowed : 15.27 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 3297 helix: 1.63 (0.20), residues: 705 sheet: 0.34 (0.19), residues: 738 loop : -0.97 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 847 TYR 0.015 0.001 TYR B 265 PHE 0.013 0.001 PHE B 192 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00489 (27492) covalent geometry : angle 0.67520 (37407) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.03121 ( 84) hydrogen bonds : bond 0.12023 ( 1091) hydrogen bonds : angle 6.97285 ( 3009) link_BETA1-3 : bond 0.02017 ( 3) link_BETA1-3 : angle 3.68648 ( 9) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 3.78609 ( 36) link_BETA1-6 : bond 0.00483 ( 3) link_BETA1-6 : angle 1.26308 ( 9) link_NAG-ASN : bond 0.00475 ( 48) link_NAG-ASN : angle 4.29093 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.7472 (t0) cc_final: 0.7098 (p0) REVERT: A 904 TYR cc_start: 0.7216 (t80) cc_final: 0.6937 (t80) REVERT: A 957 GLN cc_start: 0.8053 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 986 LYS cc_start: 0.8182 (tttp) cc_final: 0.7821 (ttpt) REVERT: B 986 LYS cc_start: 0.8218 (tttp) cc_final: 0.7875 (ttpt) REVERT: B 1113 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8140 (mm110) REVERT: C 118 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8567 (tp) REVERT: C 281 GLU cc_start: 0.8526 (pm20) cc_final: 0.8311 (pm20) outliers start: 29 outliers final: 18 residues processed: 256 average time/residue: 0.5590 time to fit residues: 169.1939 Evaluate side-chains 223 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 804 GLN A 957 GLN B 314 GLN B 613 GLN B 804 GLN B1054 GLN C 334 ASN C 804 GLN C 957 GLN C1113 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096621 restraints weight = 35106.380| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.48 r_work: 0.3040 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27600 Z= 0.187 Angle : 0.650 14.064 37689 Z= 0.325 Chirality : 0.048 0.398 4416 Planarity : 0.005 0.073 4752 Dihedral : 8.950 62.945 5127 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.88 % Allowed : 14.23 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3297 helix: 1.73 (0.19), residues: 690 sheet: 0.39 (0.18), residues: 777 loop : -1.05 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.026 0.002 TYR A1067 PHE 0.017 0.002 PHE C 133 TRP 0.024 0.002 TRP C 886 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00436 (27492) covalent geometry : angle 0.60264 (37407) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.44850 ( 84) hydrogen bonds : bond 0.04848 ( 1091) hydrogen bonds : angle 5.95005 ( 3009) link_BETA1-3 : bond 0.01872 ( 3) link_BETA1-3 : angle 3.90746 ( 9) link_BETA1-4 : bond 0.00165 ( 12) link_BETA1-4 : angle 3.41500 ( 36) link_BETA1-6 : bond 0.00158 ( 3) link_BETA1-6 : angle 1.40866 ( 9) link_NAG-ASN : bond 0.00501 ( 48) link_NAG-ASN : angle 3.34285 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.7278 (t0) cc_final: 0.6402 (p0) REVERT: A 834 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6750 (mt) REVERT: A 841 LEU cc_start: 0.7348 (tp) cc_final: 0.7110 (tm) REVERT: A 904 TYR cc_start: 0.6978 (t80) cc_final: 0.6546 (t80) REVERT: A 964 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7961 (mtpt) REVERT: A 986 LYS cc_start: 0.7868 (tttp) cc_final: 0.7373 (ttpt) REVERT: A 1092 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6427 (mm-30) REVERT: B 197 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8317 (mm) REVERT: B 834 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6816 (mt) REVERT: B 964 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8084 (mtpt) REVERT: B 1092 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: C 104 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8303 (m-90) REVERT: C 281 GLU cc_start: 0.8560 (pm20) cc_final: 0.8157 (pm20) REVERT: C 654 GLU cc_start: 0.7564 (tt0) cc_final: 0.7101 (mt-10) REVERT: C 1092 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6368 (mm-30) outliers start: 54 outliers final: 18 residues processed: 258 average time/residue: 0.6431 time to fit residues: 196.1473 Evaluate side-chains 239 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 265 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 217 optimal weight: 0.0980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 804 GLN C 804 GLN C 957 GLN C1125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099428 restraints weight = 26244.709| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.05 r_work: 0.3113 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27600 Z= 0.146 Angle : 0.598 10.824 37689 Z= 0.298 Chirality : 0.045 0.365 4416 Planarity : 0.004 0.067 4752 Dihedral : 7.831 58.413 5106 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 14.54 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3297 helix: 1.77 (0.19), residues: 690 sheet: 0.42 (0.18), residues: 777 loop : -1.04 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 847 TYR 0.020 0.001 TYR C1067 PHE 0.014 0.001 PHE C 133 TRP 0.019 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00332 (27492) covalent geometry : angle 0.55475 (37407) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.25371 ( 84) hydrogen bonds : bond 0.04435 ( 1091) hydrogen bonds : angle 5.79714 ( 3009) link_BETA1-3 : bond 0.01818 ( 3) link_BETA1-3 : angle 3.55980 ( 9) link_BETA1-4 : bond 0.00303 ( 12) link_BETA1-4 : angle 3.48043 ( 36) link_BETA1-6 : bond 0.00331 ( 3) link_BETA1-6 : angle 1.20715 ( 9) link_NAG-ASN : bond 0.00559 ( 48) link_NAG-ASN : angle 2.97434 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: A 796 ASP cc_start: 0.7297 (t0) cc_final: 0.6492 (p0) REVERT: A 834 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.6944 (mt) REVERT: A 841 LEU cc_start: 0.7490 (tp) cc_final: 0.7243 (tm) REVERT: A 964 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8088 (mtpt) REVERT: A 986 LYS cc_start: 0.8006 (tttp) cc_final: 0.7521 (ttpt) REVERT: A 1092 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: B 755 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.5190 (mp10) REVERT: B 834 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7025 (mt) REVERT: B 964 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8132 (mtpt) REVERT: B 1092 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: C 281 GLU cc_start: 0.8640 (pm20) cc_final: 0.8246 (pm20) REVERT: C 616 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7827 (m110) REVERT: C 654 GLU cc_start: 0.7692 (tt0) cc_final: 0.7253 (mt-10) REVERT: C 776 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7611 (ttmt) REVERT: C 1092 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6492 (mm-30) outliers start: 51 outliers final: 15 residues processed: 255 average time/residue: 0.6562 time to fit residues: 197.7233 Evaluate side-chains 248 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 292 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 955 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.093903 restraints weight = 30067.500| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.22 r_work: 0.3017 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 27600 Z= 0.244 Angle : 0.696 13.541 37689 Z= 0.349 Chirality : 0.050 0.489 4416 Planarity : 0.005 0.066 4752 Dihedral : 7.751 59.955 5106 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.35 % Favored : 95.46 % Rotamer: Outliers : 2.09 % Allowed : 14.23 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3297 helix: 1.50 (0.19), residues: 690 sheet: 0.43 (0.18), residues: 777 loop : -1.12 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1039 TYR 0.025 0.002 TYR B1067 PHE 0.017 0.002 PHE A 133 TRP 0.028 0.003 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00579 (27492) covalent geometry : angle 0.64824 (37407) SS BOND : bond 0.00551 ( 42) SS BOND : angle 1.75000 ( 84) hydrogen bonds : bond 0.05267 ( 1091) hydrogen bonds : angle 6.01613 ( 3009) link_BETA1-3 : bond 0.01544 ( 3) link_BETA1-3 : angle 3.65161 ( 9) link_BETA1-4 : bond 0.00205 ( 12) link_BETA1-4 : angle 3.96771 ( 36) link_BETA1-6 : bond 0.00127 ( 3) link_BETA1-6 : angle 1.43044 ( 9) link_NAG-ASN : bond 0.00621 ( 48) link_NAG-ASN : angle 3.32526 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7862 (mtp85) REVERT: A 780 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: A 796 ASP cc_start: 0.7288 (t0) cc_final: 0.6325 (p0) REVERT: A 834 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6916 (mt) REVERT: A 904 TYR cc_start: 0.6953 (t80) cc_final: 0.6411 (t80) REVERT: A 964 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7936 (mtpt) REVERT: A 986 LYS cc_start: 0.7848 (tttp) cc_final: 0.7323 (ttpt) REVERT: A 1092 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6538 (mt-10) REVERT: B 177 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7125 (ttt) REVERT: B 197 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8274 (mm) REVERT: B 755 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.5161 (mp10) REVERT: B 796 ASP cc_start: 0.7220 (t0) cc_final: 0.6095 (p0) REVERT: B 834 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6941 (mt) REVERT: B 886 TRP cc_start: 0.7485 (p90) cc_final: 0.7259 (p90) REVERT: B 964 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: B 1092 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: C 15 CYS cc_start: 0.6910 (m) cc_final: 0.6625 (m) REVERT: C 104 TRP cc_start: 0.9113 (OUTLIER) cc_final: 0.8494 (m-90) REVERT: C 190 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7643 (tpt170) REVERT: C 616 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7699 (m110) REVERT: C 654 GLU cc_start: 0.7537 (tt0) cc_final: 0.7069 (mt-10) REVERT: C 776 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7206 (ttmt) REVERT: C 834 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6892 (mt) REVERT: C 1092 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6596 (mm-30) outliers start: 60 outliers final: 24 residues processed: 264 average time/residue: 0.6541 time to fit residues: 203.5168 Evaluate side-chains 264 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096375 restraints weight = 33496.988| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.28 r_work: 0.3061 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27600 Z= 0.165 Angle : 0.622 12.732 37689 Z= 0.310 Chirality : 0.047 0.481 4416 Planarity : 0.004 0.061 4752 Dihedral : 7.318 57.901 5106 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.95 % Rotamer: Outliers : 1.77 % Allowed : 14.96 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.14), residues: 3297 helix: 1.61 (0.19), residues: 690 sheet: 0.42 (0.18), residues: 777 loop : -1.13 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 403 TYR 0.021 0.001 TYR A1067 PHE 0.014 0.001 PHE A 133 TRP 0.019 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00378 (27492) covalent geometry : angle 0.57469 (37407) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.47625 ( 84) hydrogen bonds : bond 0.04576 ( 1091) hydrogen bonds : angle 5.81434 ( 3009) link_BETA1-3 : bond 0.01655 ( 3) link_BETA1-3 : angle 3.47900 ( 9) link_BETA1-4 : bond 0.00251 ( 12) link_BETA1-4 : angle 3.78123 ( 36) link_BETA1-6 : bond 0.00215 ( 3) link_BETA1-6 : angle 1.26940 ( 9) link_NAG-ASN : bond 0.00563 ( 48) link_NAG-ASN : angle 3.14572 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: A 780 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: A 796 ASP cc_start: 0.7391 (t0) cc_final: 0.6488 (p0) REVERT: A 834 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7147 (mt) REVERT: A 904 TYR cc_start: 0.7320 (t80) cc_final: 0.6729 (t80) REVERT: A 964 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8209 (mtpt) REVERT: A 986 LYS cc_start: 0.8088 (tttp) cc_final: 0.7587 (ttpt) REVERT: A 1092 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: B 755 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.5316 (mp10) REVERT: B 780 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: B 796 ASP cc_start: 0.7272 (t0) cc_final: 0.6178 (p0) REVERT: B 834 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7166 (mt) REVERT: B 964 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8170 (mtpt) REVERT: B 1092 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: C 15 CYS cc_start: 0.7081 (m) cc_final: 0.6766 (m) REVERT: C 104 TRP cc_start: 0.9287 (OUTLIER) cc_final: 0.8713 (m-90) REVERT: C 190 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.7839 (tpt170) REVERT: C 654 GLU cc_start: 0.7828 (tt0) cc_final: 0.7387 (mt-10) REVERT: C 776 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7707 (ttmt) REVERT: C 834 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7099 (mt) REVERT: C 1092 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6668 (mm-30) outliers start: 51 outliers final: 22 residues processed: 256 average time/residue: 0.6487 time to fit residues: 196.5462 Evaluate side-chains 256 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 230 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 317 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 253 optimal weight: 0.6980 chunk 123 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094105 restraints weight = 29300.304| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.19 r_work: 0.3021 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27600 Z= 0.241 Angle : 0.685 14.141 37689 Z= 0.342 Chirality : 0.050 0.596 4416 Planarity : 0.005 0.060 4752 Dihedral : 7.441 59.554 5103 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.05 % Favored : 95.77 % Rotamer: Outliers : 1.95 % Allowed : 14.82 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.14), residues: 3297 helix: 1.50 (0.19), residues: 690 sheet: 0.43 (0.18), residues: 777 loop : -1.17 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.024 0.002 TYR B1067 PHE 0.015 0.002 PHE C 133 TRP 0.032 0.003 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00569 (27492) covalent geometry : angle 0.63633 (37407) SS BOND : bond 0.00595 ( 42) SS BOND : angle 1.74588 ( 84) hydrogen bonds : bond 0.05121 ( 1091) hydrogen bonds : angle 5.95236 ( 3009) link_BETA1-3 : bond 0.01542 ( 3) link_BETA1-3 : angle 3.48279 ( 9) link_BETA1-4 : bond 0.00216 ( 12) link_BETA1-4 : angle 4.02479 ( 36) link_BETA1-6 : bond 0.00136 ( 3) link_BETA1-6 : angle 1.37775 ( 9) link_NAG-ASN : bond 0.00743 ( 48) link_NAG-ASN : angle 3.30989 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7843 (mtp85) REVERT: A 780 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: A 796 ASP cc_start: 0.7301 (t0) cc_final: 0.6190 (p0) REVERT: A 834 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6931 (mt) REVERT: A 904 TYR cc_start: 0.6947 (t80) cc_final: 0.6338 (t80) REVERT: A 964 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: A 986 LYS cc_start: 0.7859 (tttp) cc_final: 0.7336 (ttpt) REVERT: A 1092 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: B 796 ASP cc_start: 0.7162 (t0) cc_final: 0.6030 (p0) REVERT: B 834 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.6978 (mt) REVERT: B 964 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7811 (mtpt) REVERT: B 1092 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: C 15 CYS cc_start: 0.6852 (m) cc_final: 0.6576 (m) REVERT: C 104 TRP cc_start: 0.9112 (OUTLIER) cc_final: 0.8477 (m-90) REVERT: C 153 MET cc_start: 0.8244 (mtm) cc_final: 0.7956 (mtp) REVERT: C 190 ARG cc_start: 0.8014 (tpp-160) cc_final: 0.7552 (tpt170) REVERT: C 654 GLU cc_start: 0.7558 (tt0) cc_final: 0.7128 (mt-10) REVERT: C 776 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7258 (ttmt) REVERT: C 834 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.6977 (mt) REVERT: C 1092 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6676 (mm-30) outliers start: 54 outliers final: 24 residues processed: 258 average time/residue: 0.6672 time to fit residues: 203.0360 Evaluate side-chains 253 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 191 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096684 restraints weight = 26026.885| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.06 r_work: 0.3063 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27600 Z= 0.165 Angle : 0.628 14.628 37689 Z= 0.312 Chirality : 0.047 0.508 4416 Planarity : 0.004 0.059 4752 Dihedral : 7.142 57.684 5103 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.88 % Allowed : 14.89 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.14), residues: 3297 helix: 1.61 (0.19), residues: 690 sheet: 0.40 (0.18), residues: 777 loop : -1.15 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 408 TYR 0.020 0.001 TYR C1067 PHE 0.013 0.001 PHE B1121 TRP 0.035 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00378 (27492) covalent geometry : angle 0.58014 (37407) SS BOND : bond 0.00440 ( 42) SS BOND : angle 1.46495 ( 84) hydrogen bonds : bond 0.04565 ( 1091) hydrogen bonds : angle 5.80228 ( 3009) link_BETA1-3 : bond 0.01633 ( 3) link_BETA1-3 : angle 3.43229 ( 9) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 3.82851 ( 36) link_BETA1-6 : bond 0.00196 ( 3) link_BETA1-6 : angle 1.30348 ( 9) link_NAG-ASN : bond 0.00703 ( 48) link_NAG-ASN : angle 3.17040 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: A 780 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: A 796 ASP cc_start: 0.7210 (t0) cc_final: 0.6085 (p0) REVERT: A 834 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6930 (mt) REVERT: A 904 TYR cc_start: 0.6890 (t80) cc_final: 0.6263 (t80) REVERT: A 921 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: A 964 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: A 1092 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: B 197 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 755 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.5088 (mp10) REVERT: B 796 ASP cc_start: 0.7107 (t0) cc_final: 0.5971 (p0) REVERT: B 834 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.6977 (mt) REVERT: B 964 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7807 (mtpt) REVERT: B 1092 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: C 15 CYS cc_start: 0.6835 (m) cc_final: 0.6554 (m) REVERT: C 104 TRP cc_start: 0.9077 (OUTLIER) cc_final: 0.8452 (m-90) REVERT: C 153 MET cc_start: 0.8261 (mtm) cc_final: 0.7975 (mtp) REVERT: C 190 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7508 (tpt170) REVERT: C 654 GLU cc_start: 0.7521 (tt0) cc_final: 0.7072 (mt-10) REVERT: C 776 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7232 (ttmt) REVERT: C 834 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6990 (mt) REVERT: C 1092 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6632 (mm-30) outliers start: 52 outliers final: 24 residues processed: 256 average time/residue: 0.6507 time to fit residues: 196.5451 Evaluate side-chains 255 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 305 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093680 restraints weight = 28718.036| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.16 r_work: 0.3013 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 27600 Z= 0.259 Angle : 0.705 15.582 37689 Z= 0.351 Chirality : 0.050 0.545 4416 Planarity : 0.005 0.059 4752 Dihedral : 7.389 59.995 5103 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 1.91 % Allowed : 14.72 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.14), residues: 3297 helix: 1.45 (0.19), residues: 690 sheet: 0.31 (0.17), residues: 816 loop : -1.18 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 403 TYR 0.024 0.002 TYR B1067 PHE 0.016 0.002 PHE C 133 TRP 0.041 0.003 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00612 (27492) covalent geometry : angle 0.65416 (37407) SS BOND : bond 0.00597 ( 42) SS BOND : angle 1.71553 ( 84) hydrogen bonds : bond 0.05267 ( 1091) hydrogen bonds : angle 5.99832 ( 3009) link_BETA1-3 : bond 0.01516 ( 3) link_BETA1-3 : angle 3.49769 ( 9) link_BETA1-4 : bond 0.00202 ( 12) link_BETA1-4 : angle 4.14739 ( 36) link_BETA1-6 : bond 0.00049 ( 3) link_BETA1-6 : angle 1.39437 ( 9) link_NAG-ASN : bond 0.00755 ( 48) link_NAG-ASN : angle 3.46897 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: A 796 ASP cc_start: 0.7258 (t0) cc_final: 0.6134 (p0) REVERT: A 834 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7042 (mt) REVERT: A 904 TYR cc_start: 0.6943 (t80) cc_final: 0.6386 (t80) REVERT: A 921 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7833 (mtmt) REVERT: A 964 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8013 (mtpt) REVERT: A 986 LYS cc_start: 0.7907 (tttp) cc_final: 0.7373 (ttpt) REVERT: A 1092 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: B 197 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8340 (mm) REVERT: B 796 ASP cc_start: 0.7268 (t0) cc_final: 0.6149 (p0) REVERT: B 834 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7111 (mt) REVERT: B 886 TRP cc_start: 0.7484 (p90) cc_final: 0.7264 (p90) REVERT: B 964 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7921 (mtpt) REVERT: B 1092 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: C 15 CYS cc_start: 0.6958 (m) cc_final: 0.6687 (m) REVERT: C 104 TRP cc_start: 0.9158 (OUTLIER) cc_final: 0.8532 (m-90) REVERT: C 153 MET cc_start: 0.8368 (mtm) cc_final: 0.8021 (mtp) REVERT: C 190 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.7614 (tpt170) REVERT: C 654 GLU cc_start: 0.7616 (tt0) cc_final: 0.7184 (mt-10) REVERT: C 776 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7363 (ttmt) REVERT: C 834 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7126 (mt) REVERT: C 1092 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6592 (mt-10) outliers start: 52 outliers final: 27 residues processed: 264 average time/residue: 0.6664 time to fit residues: 206.9210 Evaluate side-chains 264 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 297 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN B 804 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096543 restraints weight = 30724.457| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.19 r_work: 0.3073 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27600 Z= 0.184 Angle : 0.647 15.500 37689 Z= 0.321 Chirality : 0.049 0.647 4416 Planarity : 0.004 0.058 4752 Dihedral : 7.136 58.294 5103 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.07 % Rotamer: Outliers : 1.81 % Allowed : 14.89 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3297 helix: 1.54 (0.19), residues: 690 sheet: 0.28 (0.18), residues: 816 loop : -1.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.021 0.002 TYR C1067 PHE 0.014 0.001 PHE C 133 TRP 0.036 0.002 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00427 (27492) covalent geometry : angle 0.59669 (37407) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.44839 ( 84) hydrogen bonds : bond 0.04714 ( 1091) hydrogen bonds : angle 5.84483 ( 3009) link_BETA1-3 : bond 0.01639 ( 3) link_BETA1-3 : angle 3.39889 ( 9) link_BETA1-4 : bond 0.00251 ( 12) link_BETA1-4 : angle 3.91426 ( 36) link_BETA1-6 : bond 0.00150 ( 3) link_BETA1-6 : angle 1.31443 ( 9) link_NAG-ASN : bond 0.00759 ( 48) link_NAG-ASN : angle 3.35479 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: A 834 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7242 (mt) REVERT: A 904 TYR cc_start: 0.7297 (t80) cc_final: 0.6777 (t80) REVERT: A 921 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8142 (mtmt) REVERT: A 964 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8282 (mtpt) REVERT: A 1029 MET cc_start: 0.8733 (tpp) cc_final: 0.8503 (tpp) REVERT: A 1092 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: B 197 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8606 (mm) REVERT: B 755 GLN cc_start: 0.6810 (OUTLIER) cc_final: 0.5327 (mp10) REVERT: B 796 ASP cc_start: 0.7342 (t0) cc_final: 0.6314 (p0) REVERT: B 804 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7558 (tp-100) REVERT: B 834 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7308 (mt) REVERT: B 935 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6758 (tp40) REVERT: B 964 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8184 (mtpt) REVERT: C 15 CYS cc_start: 0.7123 (m) cc_final: 0.6831 (m) REVERT: C 104 TRP cc_start: 0.9320 (OUTLIER) cc_final: 0.8750 (m-90) REVERT: C 153 MET cc_start: 0.8417 (mtm) cc_final: 0.8088 (mtp) REVERT: C 190 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.7892 (tpt170) REVERT: C 654 GLU cc_start: 0.7905 (tt0) cc_final: 0.7495 (mt-10) REVERT: C 776 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7845 (ttmt) REVERT: C 834 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7351 (mt) REVERT: C 1092 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6711 (mt-10) outliers start: 49 outliers final: 25 residues processed: 262 average time/residue: 0.6768 time to fit residues: 209.3595 Evaluate side-chains 263 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 2 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 0.0770 chunk 329 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097292 restraints weight = 26592.667| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3088 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 27600 Z= 0.213 Angle : 0.785 59.037 37689 Z= 0.417 Chirality : 0.050 0.724 4416 Planarity : 0.004 0.058 4752 Dihedral : 7.130 58.314 5103 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 1.60 % Allowed : 15.17 % Favored : 83.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3297 helix: 1.54 (0.19), residues: 690 sheet: 0.28 (0.18), residues: 816 loop : -1.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.027 0.002 TYR B 904 PHE 0.026 0.002 PHE B 817 TRP 0.033 0.002 TRP C 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00482 (27492) covalent geometry : angle 0.73326 (37407) SS BOND : bond 0.00823 ( 42) SS BOND : angle 2.83356 ( 84) hydrogen bonds : bond 0.04719 ( 1091) hydrogen bonds : angle 5.84581 ( 3009) link_BETA1-3 : bond 0.01444 ( 3) link_BETA1-3 : angle 3.44728 ( 9) link_BETA1-4 : bond 0.00249 ( 12) link_BETA1-4 : angle 3.92210 ( 36) link_BETA1-6 : bond 0.00097 ( 3) link_BETA1-6 : angle 1.32066 ( 9) link_NAG-ASN : bond 0.00905 ( 48) link_NAG-ASN : angle 3.52142 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: A 834 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7250 (mt) REVERT: A 904 TYR cc_start: 0.7273 (t80) cc_final: 0.6760 (t80) REVERT: A 921 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8134 (mtmt) REVERT: A 964 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: A 1092 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6735 (mt-10) REVERT: B 197 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 755 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.5315 (mp10) REVERT: B 796 ASP cc_start: 0.7332 (t0) cc_final: 0.6310 (p0) REVERT: B 804 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6252 (tm130) REVERT: B 834 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7318 (mt) REVERT: B 964 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8180 (mtpt) REVERT: C 15 CYS cc_start: 0.7104 (m) cc_final: 0.6811 (m) REVERT: C 104 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.8745 (m-90) REVERT: C 153 MET cc_start: 0.8412 (mtm) cc_final: 0.8082 (mtp) REVERT: C 190 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.7875 (tpt170) REVERT: C 654 GLU cc_start: 0.7886 (tt0) cc_final: 0.7476 (mt-10) REVERT: C 776 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7844 (ttmt) REVERT: C 834 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7353 (mt) REVERT: C 1092 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6707 (mt-10) outliers start: 43 outliers final: 25 residues processed: 253 average time/residue: 0.6749 time to fit residues: 201.7662 Evaluate side-chains 263 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 957 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.096810 restraints weight = 28955.129| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.12 r_work: 0.3079 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 27600 Z= 0.197 Angle : 0.770 59.197 37689 Z= 0.402 Chirality : 0.049 0.622 4416 Planarity : 0.004 0.058 4752 Dihedral : 7.126 58.309 5103 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.64 % Allowed : 15.21 % Favored : 83.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3297 helix: 1.55 (0.19), residues: 690 sheet: 0.28 (0.18), residues: 816 loop : -1.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.023 0.002 TYR B 904 PHE 0.013 0.002 PHE C 133 TRP 0.038 0.002 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00462 (27492) covalent geometry : angle 0.72172 (37407) SS BOND : bond 0.00484 ( 42) SS BOND : angle 2.48922 ( 84) hydrogen bonds : bond 0.04723 ( 1091) hydrogen bonds : angle 5.84541 ( 3009) link_BETA1-3 : bond 0.01696 ( 3) link_BETA1-3 : angle 3.38582 ( 9) link_BETA1-4 : bond 0.00308 ( 12) link_BETA1-4 : angle 3.92599 ( 36) link_BETA1-6 : bond 0.00095 ( 3) link_BETA1-6 : angle 1.27604 ( 9) link_NAG-ASN : bond 0.01108 ( 48) link_NAG-ASN : angle 3.42069 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15570.26 seconds wall clock time: 265 minutes 22.56 seconds (15922.56 seconds total)