Starting phenix.real_space_refine on Mon Jun 23 20:07:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qur_14152/06_2025/7qur_14152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qur_14152/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qur_14152/06_2025/7qur_14152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qur_14152/06_2025/7qur_14152.map" model { file = "/net/cci-nas-00/data/ceres_data/7qur_14152/06_2025/7qur_14152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qur_14152/06_2025/7qur_14152.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 25.59, per 1000 atoms: 0.94 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: 7.02 Conformation dependent library (CDL) restraints added in 6.3 seconds 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: 4.36 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: 13.66 Time building geometry restraints manager: 7.95 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: 0.08 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: 4.790 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: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 78.720 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.220 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), 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 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B 192 TYR 0.015 0.001 TYR B 265 ARG 0.007 0.000 ARG A 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 48) link_NAG-ASN : angle 4.29093 ( 144) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 3.78609 ( 36) hydrogen bonds : bond 0.12023 ( 1091) hydrogen bonds : angle 6.97285 ( 3009) link_BETA1-6 : bond 0.00483 ( 3) link_BETA1-6 : angle 1.26308 ( 9) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.03121 ( 84) link_BETA1-3 : bond 0.02017 ( 3) link_BETA1-3 : angle 3.68648 ( 9) covalent geometry : bond 0.00489 (27492) covalent geometry : angle 0.67520 (37407) *********************** 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 : 2.759 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 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: 0.8141 (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: 1.2743 time to fit residues: 387.9216 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 : 3.060 ------------------------------------------------------------------------------- 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 278 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 258 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 0.0470 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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 314 GLN C 334 ASN C 613 GLN C 804 GLN C 957 GLN C1113 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098548 restraints weight = 39501.885| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.51 r_work: 0.3084 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27600 Z= 0.146 Angle : 0.610 13.497 37689 Z= 0.304 Chirality : 0.046 0.393 4416 Planarity : 0.004 0.073 4752 Dihedral : 8.839 61.514 5127 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.67 % Allowed : 14.47 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3297 helix: 1.84 (0.19), residues: 690 sheet: 0.44 (0.18), residues: 747 loop : -1.03 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS A1088 PHE 0.014 0.001 PHE A 133 TYR 0.024 0.001 TYR B1067 ARG 0.003 0.000 ARG C 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 48) link_NAG-ASN : angle 3.20510 ( 144) link_BETA1-4 : bond 0.00316 ( 12) link_BETA1-4 : angle 3.16431 ( 36) hydrogen bonds : bond 0.04451 ( 1091) hydrogen bonds : angle 5.84775 ( 3009) link_BETA1-6 : bond 0.00278 ( 3) link_BETA1-6 : angle 1.42447 ( 9) SS BOND : bond 0.00399 ( 42) SS BOND : angle 1.24439 ( 84) link_BETA1-3 : bond 0.01916 ( 3) link_BETA1-3 : angle 4.18719 ( 9) covalent geometry : bond 0.00331 (27492) covalent geometry : angle 0.56332 (37407) *********************** 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 272 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 654 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 780 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: A 796 ASP cc_start: 0.7310 (t0) cc_final: 0.6445 (p0) REVERT: A 834 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6696 (mt) REVERT: A 841 LEU cc_start: 0.7337 (tp) cc_final: 0.7108 (tm) REVERT: A 964 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7953 (mtpt) REVERT: A 986 LYS cc_start: 0.7872 (tttp) cc_final: 0.7388 (ttpt) REVERT: B 654 GLU cc_start: 0.7713 (tt0) cc_final: 0.7474 (mt-10) REVERT: B 834 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.6754 (mt) REVERT: B 1113 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7758 (mm110) REVERT: C 281 GLU cc_start: 0.8564 (pm20) cc_final: 0.8169 (pm20) REVERT: C 654 GLU cc_start: 0.7563 (tt0) cc_final: 0.7100 (mt-10) outliers start: 48 outliers final: 16 residues processed: 257 average time/residue: 1.2134 time to fit residues: 371.3873 Evaluate side-chains 235 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 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 1127 ASP 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 1010 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 177 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 152 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 334 ASN C 804 GLN C 957 GLN C1125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096232 restraints weight = 28034.414| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.15 r_work: 0.3053 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27600 Z= 0.189 Angle : 0.646 12.521 37689 Z= 0.323 Chirality : 0.047 0.391 4416 Planarity : 0.004 0.068 4752 Dihedral : 7.899 58.298 5106 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 1.98 % Allowed : 14.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3297 helix: 1.69 (0.19), residues: 690 sheet: 0.41 (0.18), residues: 777 loop : -1.05 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.016 0.002 PHE A 817 TYR 0.023 0.002 TYR C1067 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 48) link_NAG-ASN : angle 3.21509 ( 144) link_BETA1-4 : bond 0.00256 ( 12) link_BETA1-4 : angle 3.69642 ( 36) hydrogen bonds : bond 0.04941 ( 1091) hydrogen bonds : angle 5.92110 ( 3009) link_BETA1-6 : bond 0.00241 ( 3) link_BETA1-6 : angle 1.32460 ( 9) SS BOND : bond 0.00428 ( 42) SS BOND : angle 1.44623 ( 84) link_BETA1-3 : bond 0.01635 ( 3) link_BETA1-3 : angle 3.60965 ( 9) covalent geometry : bond 0.00438 (27492) covalent geometry : angle 0.59974 (37407) *********************** 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 284 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7798 (m-40) REVERT: A 796 ASP cc_start: 0.7217 (t0) cc_final: 0.6327 (p0) REVERT: A 834 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6792 (mt) REVERT: A 964 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: A 986 LYS cc_start: 0.7826 (tttp) cc_final: 0.7323 (ttpt) REVERT: A 1092 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: B 197 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (mm) REVERT: B 616 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7554 (m110) REVERT: B 654 GLU cc_start: 0.7551 (tt0) cc_final: 0.7330 (mt-10) REVERT: B 796 ASP cc_start: 0.7186 (t0) cc_final: 0.6048 (p0) REVERT: B 834 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6863 (mt) REVERT: B 1092 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: C 104 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8357 (m-90) REVERT: C 281 GLU cc_start: 0.8504 (pm20) cc_final: 0.8059 (pm20) REVERT: C 616 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7765 (m110) REVERT: C 654 GLU cc_start: 0.7456 (tt0) cc_final: 0.7006 (mt-10) REVERT: C 697 MET cc_start: 0.8677 (ptt) cc_final: 0.8472 (ptm) REVERT: C 776 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7238 (ttmt) REVERT: C 834 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6859 (mt) REVERT: C 1092 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6453 (mm-30) outliers start: 57 outliers final: 18 residues processed: 260 average time/residue: 1.4038 time to fit residues: 435.4213 Evaluate side-chains 257 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 2.850 ------------------------------------------------------------------------------- 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 616 ASN 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 616 ASN 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 834 ILE 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 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 834 ILE 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 306 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 181 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN 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 = 0.3739 r_free = 0.3739 target = 0.137831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098312 restraints weight = 33706.735| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.30 r_work: 0.3092 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27600 Z= 0.131 Angle : 0.586 13.913 37689 Z= 0.292 Chirality : 0.046 0.476 4416 Planarity : 0.004 0.063 4752 Dihedral : 7.258 58.040 5106 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.29 % Rotamer: Outliers : 1.70 % Allowed : 14.58 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3297 helix: 1.79 (0.19), residues: 690 sheet: 0.40 (0.18), residues: 762 loop : -1.04 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 PHE 0.016 0.001 PHE A 817 TYR 0.019 0.001 TYR A1067 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 48) link_NAG-ASN : angle 3.08530 ( 144) link_BETA1-4 : bond 0.00281 ( 12) link_BETA1-4 : angle 3.44642 ( 36) hydrogen bonds : bond 0.04208 ( 1091) hydrogen bonds : angle 5.70642 ( 3009) link_BETA1-6 : bond 0.00270 ( 3) link_BETA1-6 : angle 1.23419 ( 9) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.23478 ( 84) link_BETA1-3 : bond 0.01764 ( 3) link_BETA1-3 : angle 3.53915 ( 9) covalent geometry : bond 0.00293 (27492) covalent geometry : angle 0.53936 (37407) *********************** 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 282 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (mtp85) REVERT: A 780 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 796 ASP cc_start: 0.7271 (t0) cc_final: 0.6399 (p0) REVERT: A 834 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.6949 (mt) REVERT: A 904 TYR cc_start: 0.7092 (t80) cc_final: 0.6596 (t80) REVERT: A 964 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8220 (mtpt) REVERT: A 986 LYS cc_start: 0.8059 (tttp) cc_final: 0.7576 (ttpt) REVERT: A 1092 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6586 (mm-30) REVERT: B 15 CYS cc_start: 0.7189 (m) cc_final: 0.6900 (m) REVERT: B 177 MET cc_start: 0.7726 (tmm) cc_final: 0.7242 (ttt) REVERT: B 190 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.8069 (tpp-160) REVERT: B 661 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 755 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.5301 (mp10) REVERT: B 796 ASP cc_start: 0.7212 (t0) cc_final: 0.6058 (p0) REVERT: B 834 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7014 (mt) REVERT: B 964 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: B 1092 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6712 (mt-10) REVERT: C 15 CYS cc_start: 0.7012 (m) cc_final: 0.6682 (m) REVERT: C 104 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.8582 (m-90) REVERT: C 190 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7831 (tpt170) REVERT: C 281 GLU cc_start: 0.8688 (pm20) cc_final: 0.8307 (pm20) REVERT: C 616 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7728 (m110) REVERT: C 654 GLU cc_start: 0.7797 (tt0) cc_final: 0.7359 (mt-10) REVERT: C 776 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7689 (ttmt) REVERT: C 834 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.6993 (mt) REVERT: C 1092 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6532 (mm-30) outliers start: 49 outliers final: 19 residues processed: 263 average time/residue: 1.3195 time to fit residues: 412.1338 Evaluate side-chains 255 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 242 LEU 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 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU 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 104 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 210 ILE 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 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 131 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 302 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094497 restraints weight = 33479.914| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.28 r_work: 0.3033 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 27600 Z= 0.245 Angle : 0.687 13.660 37689 Z= 0.343 Chirality : 0.049 0.494 4416 Planarity : 0.005 0.062 4752 Dihedral : 7.469 59.604 5106 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 2.02 % Allowed : 14.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3297 helix: 1.55 (0.19), residues: 690 sheet: 0.45 (0.18), residues: 777 loop : -1.10 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 886 HIS 0.004 0.001 HIS A 66 PHE 0.015 0.002 PHE C 133 TYR 0.025 0.002 TYR A1067 ARG 0.005 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 48) link_NAG-ASN : angle 3.32249 ( 144) link_BETA1-4 : bond 0.00206 ( 12) link_BETA1-4 : angle 3.90960 ( 36) hydrogen bonds : bond 0.05165 ( 1091) hydrogen bonds : angle 5.95482 ( 3009) link_BETA1-6 : bond 0.00157 ( 3) link_BETA1-6 : angle 1.37480 ( 9) SS BOND : bond 0.00631 ( 42) SS BOND : angle 1.89140 ( 84) link_BETA1-3 : bond 0.01551 ( 3) link_BETA1-3 : angle 3.53933 ( 9) covalent geometry : bond 0.00579 (27492) covalent geometry : angle 0.63798 (37407) *********************** 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 288 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8165 (mtp85) REVERT: A 780 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: A 796 ASP cc_start: 0.7437 (t0) cc_final: 0.6531 (p0) REVERT: A 834 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7128 (mt) REVERT: A 904 TYR cc_start: 0.7194 (t80) cc_final: 0.6813 (t80) REVERT: A 964 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8245 (mtpt) REVERT: A 986 LYS cc_start: 0.8110 (tttp) cc_final: 0.7611 (ttpt) REVERT: A 1092 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: B 15 CYS cc_start: 0.7331 (m) cc_final: 0.7071 (m) REVERT: B 197 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 661 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 780 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: B 796 ASP cc_start: 0.7311 (t0) cc_final: 0.6269 (p0) REVERT: B 834 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7169 (mt) REVERT: B 964 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8228 (mtpt) REVERT: B 1092 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: C 15 CYS cc_start: 0.7085 (m) cc_final: 0.6793 (m) REVERT: C 104 TRP cc_start: 0.9306 (OUTLIER) cc_final: 0.8725 (m-90) REVERT: C 190 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.7921 (tpt170) REVERT: C 616 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7873 (m110) REVERT: C 654 GLU cc_start: 0.7780 (tt0) cc_final: 0.7348 (mt-10) REVERT: C 776 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7743 (ttmt) REVERT: C 834 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7069 (mt) outliers start: 58 outliers final: 23 residues processed: 265 average time/residue: 1.2535 time to fit residues: 394.0601 Evaluate side-chains 260 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 2.869 ------------------------------------------------------------------------------- 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 212 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 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 661 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 780 GLU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 240 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.135929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095979 restraints weight = 33806.845| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.29 r_work: 0.3056 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27600 Z= 0.178 Angle : 0.635 13.316 37689 Z= 0.316 Chirality : 0.047 0.427 4416 Planarity : 0.004 0.057 4752 Dihedral : 7.156 57.987 5104 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 1.84 % Allowed : 14.96 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3297 helix: 1.61 (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 TRP 0.029 0.002 TRP C 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B1121 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 48) link_NAG-ASN : angle 3.22034 ( 144) link_BETA1-4 : bond 0.00250 ( 12) link_BETA1-4 : angle 3.77139 ( 36) hydrogen bonds : bond 0.04648 ( 1091) hydrogen bonds : angle 5.82732 ( 3009) link_BETA1-6 : bond 0.00213 ( 3) link_BETA1-6 : angle 1.26306 ( 9) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.63575 ( 84) link_BETA1-3 : bond 0.01651 ( 3) link_BETA1-3 : angle 3.40024 ( 9) covalent geometry : bond 0.00414 (27492) covalent geometry : angle 0.58650 (37407) *********************** 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: 52 poor density : 223 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8128 (mtp85) REVERT: A 780 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: A 796 ASP cc_start: 0.7393 (t0) cc_final: 0.6410 (p0) REVERT: A 834 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7135 (mt) REVERT: A 904 TYR cc_start: 0.7146 (t80) cc_final: 0.6769 (t80) REVERT: A 921 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8087 (mtmt) REVERT: A 964 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8235 (mtpt) REVERT: A 986 LYS cc_start: 0.8088 (tttp) cc_final: 0.7588 (ttpt) REVERT: A 1092 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: B 197 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8520 (mm) REVERT: B 661 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: B 755 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.5313 (mp10) REVERT: B 780 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: B 796 ASP cc_start: 0.7278 (t0) cc_final: 0.6236 (p0) REVERT: B 834 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7147 (mt) REVERT: B 964 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8163 (mtpt) REVERT: B 1092 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: C 15 CYS cc_start: 0.7050 (m) cc_final: 0.6760 (m) REVERT: C 104 TRP cc_start: 0.9293 (OUTLIER) cc_final: 0.8723 (m-90) REVERT: C 190 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7813 (tpt170) REVERT: C 616 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7738 (m110) REVERT: C 654 GLU cc_start: 0.7839 (tt0) cc_final: 0.7399 (mt-10) REVERT: C 776 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7720 (ttmt) REVERT: C 834 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7081 (mt) outliers start: 52 outliers final: 24 residues processed: 255 average time/residue: 1.2901 time to fit residues: 394.1868 Evaluate side-chains 262 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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 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 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 661 GLU 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 776 LYS 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 197 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 616 ASN 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 219 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 804 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.133144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092677 restraints weight = 32487.066| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.37 r_work: 0.2981 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 27600 Z= 0.316 Angle : 0.749 14.757 37689 Z= 0.374 Chirality : 0.052 0.487 4416 Planarity : 0.005 0.059 4752 Dihedral : 7.554 58.932 5103 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 1.95 % Allowed : 14.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3297 helix: 1.34 (0.19), residues: 690 sheet: 0.42 (0.18), residues: 789 loop : -1.21 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 886 HIS 0.005 0.001 HIS A 66 PHE 0.017 0.002 PHE C1121 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 48) link_NAG-ASN : angle 3.61649 ( 144) link_BETA1-4 : bond 0.00166 ( 12) link_BETA1-4 : angle 4.29032 ( 36) hydrogen bonds : bond 0.05613 ( 1091) hydrogen bonds : angle 6.09795 ( 3009) link_BETA1-6 : bond 0.00048 ( 3) link_BETA1-6 : angle 1.43400 ( 9) SS BOND : bond 0.00700 ( 42) SS BOND : angle 2.02001 ( 84) link_BETA1-3 : bond 0.01414 ( 3) link_BETA1-3 : angle 3.52226 ( 9) covalent geometry : bond 0.00753 (27492) covalent geometry : angle 0.69637 (37407) *********************** 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 284 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 796 ASP cc_start: 0.7283 (t0) cc_final: 0.6140 (p0) REVERT: A 834 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7017 (mt) REVERT: A 964 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: A 986 LYS cc_start: 0.7951 (tttp) cc_final: 0.7428 (ttpt) REVERT: A 1092 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: B 197 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8319 (mm) REVERT: B 780 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 796 ASP cc_start: 0.7280 (t0) cc_final: 0.6136 (p0) REVERT: B 834 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7063 (mt) REVERT: B 964 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.8001 (mtpt) REVERT: B 1092 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6880 (mt-10) REVERT: C 15 CYS cc_start: 0.6911 (m) cc_final: 0.6638 (m) REVERT: C 104 TRP cc_start: 0.9163 (OUTLIER) cc_final: 0.8559 (m-90) REVERT: C 153 MET cc_start: 0.8344 (mtm) cc_final: 0.7954 (mtp) REVERT: C 616 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7724 (m110) REVERT: C 776 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7302 (ttmt) REVERT: C 834 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7050 (mt) outliers start: 53 outliers final: 24 residues processed: 267 average time/residue: 1.2715 time to fit residues: 402.4814 Evaluate side-chains 264 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 212 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 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 776 LYS 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 161 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 233 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 274 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.136408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.097968 restraints weight = 27239.752| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.06 r_work: 0.3097 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27600 Z= 0.166 Angle : 0.629 14.521 37689 Z= 0.312 Chirality : 0.047 0.543 4416 Planarity : 0.004 0.057 4752 Dihedral : 7.062 57.787 5103 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 1.60 % Allowed : 15.00 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3297 helix: 1.57 (0.19), residues: 690 sheet: 0.28 (0.17), residues: 816 loop : -1.16 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B1121 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG B1039 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 48) link_NAG-ASN : angle 3.31776 ( 144) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 3.82176 ( 36) hydrogen bonds : bond 0.04548 ( 1091) hydrogen bonds : angle 5.80754 ( 3009) link_BETA1-6 : bond 0.00195 ( 3) link_BETA1-6 : angle 1.25289 ( 9) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.44719 ( 84) link_BETA1-3 : bond 0.01646 ( 3) link_BETA1-3 : angle 3.36713 ( 9) covalent geometry : bond 0.00381 (27492) covalent geometry : angle 0.57880 (37407) *********************** 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 268 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8423 (tt0) cc_final: 0.8214 (tt0) REVERT: A 780 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: A 796 ASP cc_start: 0.7286 (t0) cc_final: 0.6242 (p0) REVERT: A 834 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7244 (mt) REVERT: A 904 TYR cc_start: 0.7197 (t80) cc_final: 0.6763 (t80) REVERT: A 964 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8258 (mtpt) REVERT: A 1092 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: B 780 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: B 796 ASP cc_start: 0.7270 (t0) cc_final: 0.6265 (p0) REVERT: B 834 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7304 (mt) REVERT: B 964 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8250 (mtpt) REVERT: C 15 CYS cc_start: 0.7134 (m) cc_final: 0.6852 (m) REVERT: C 104 TRP cc_start: 0.9309 (OUTLIER) cc_final: 0.8732 (m-90) REVERT: C 153 MET cc_start: 0.8455 (mtm) cc_final: 0.8122 (mtp) REVERT: C 190 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.7865 (tpt170) REVERT: C 654 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7916 (mt-10) REVERT: C 776 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7834 (ttmt) REVERT: C 834 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7326 (mt) outliers start: 43 outliers final: 21 residues processed: 255 average time/residue: 1.6601 time to fit residues: 506.0601 Evaluate side-chains 256 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 3.683 ------------------------------------------------------------------------------- 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 212 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 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 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 776 LYS 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 285 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 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 = 0.3733 r_free = 0.3733 target = 0.136569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.098141 restraints weight = 26532.090| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.04 r_work: 0.3101 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27600 Z= 0.164 Angle : 0.631 14.988 37689 Z= 0.313 Chirality : 0.049 0.765 4416 Planarity : 0.004 0.058 4752 Dihedral : 6.976 57.546 5103 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.60 % Allowed : 14.96 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3297 helix: 1.64 (0.19), residues: 690 sheet: 0.34 (0.18), residues: 810 loop : -1.14 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B 898 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 48) link_NAG-ASN : angle 3.31060 ( 144) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 3.80470 ( 36) hydrogen bonds : bond 0.04514 ( 1091) hydrogen bonds : angle 5.76322 ( 3009) link_BETA1-6 : bond 0.00169 ( 3) link_BETA1-6 : angle 1.29559 ( 9) SS BOND : bond 0.00422 ( 42) SS BOND : angle 1.45254 ( 84) link_BETA1-3 : bond 0.01639 ( 3) link_BETA1-3 : angle 3.44625 ( 9) covalent geometry : bond 0.00377 (27492) covalent geometry : angle 0.58095 (37407) *********************** 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 269 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8412 (tt0) cc_final: 0.8208 (tt0) REVERT: A 780 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: A 834 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7188 (mt) REVERT: A 904 TYR cc_start: 0.7197 (t80) cc_final: 0.6833 (t80) REVERT: A 964 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8286 (mtpt) REVERT: A 1092 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6691 (mt-10) REVERT: B 197 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 755 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.5286 (mp10) REVERT: B 780 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: B 796 ASP cc_start: 0.7320 (t0) cc_final: 0.6321 (p0) REVERT: B 834 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7268 (mt) REVERT: B 964 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8225 (mtpt) REVERT: C 15 CYS cc_start: 0.7126 (m) cc_final: 0.6840 (m) REVERT: C 104 TRP cc_start: 0.9328 (OUTLIER) cc_final: 0.8756 (m-90) REVERT: C 153 MET cc_start: 0.8438 (mtm) cc_final: 0.8103 (mtp) REVERT: C 190 ARG cc_start: 0.8314 (tpp-160) cc_final: 0.7866 (tpt170) REVERT: C 654 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 776 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7836 (ttmt) REVERT: C 834 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7329 (mt) outliers start: 43 outliers final: 24 residues processed: 251 average time/residue: 1.2213 time to fit residues: 365.4628 Evaluate side-chains 259 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 212 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 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 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 325 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN A 957 GLN B 804 GLN C 804 GLN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.137298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098822 restraints weight = 29374.027| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.14 r_work: 0.3110 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27600 Z= 0.132 Angle : 0.606 12.544 37689 Z= 0.300 Chirality : 0.048 0.735 4416 Planarity : 0.004 0.057 4752 Dihedral : 6.822 57.352 5103 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.59 % Favored : 96.23 % Rotamer: Outliers : 1.46 % Allowed : 15.14 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3297 helix: 1.71 (0.19), residues: 690 sheet: 0.27 (0.18), residues: 795 loop : -1.11 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE B1121 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 48) link_NAG-ASN : angle 3.13909 ( 144) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 3.65778 ( 36) hydrogen bonds : bond 0.04212 ( 1091) hydrogen bonds : angle 5.67695 ( 3009) link_BETA1-6 : bond 0.00207 ( 3) link_BETA1-6 : angle 1.26159 ( 9) SS BOND : bond 0.00367 ( 42) SS BOND : angle 1.30310 ( 84) link_BETA1-3 : bond 0.01759 ( 3) link_BETA1-3 : angle 3.36988 ( 9) covalent geometry : bond 0.00296 (27492) covalent geometry : angle 0.55843 (37407) ********************** 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: 39 poor density : 230 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLN cc_start: 0.8406 (tt0) cc_final: 0.8205 (tt0) REVERT: A 780 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: A 834 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 904 TYR cc_start: 0.7205 (t80) cc_final: 0.6809 (t80) REVERT: A 964 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8261 (mtpt) REVERT: A 1092 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: B 755 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.5296 (mp10) REVERT: B 780 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: B 796 ASP cc_start: 0.7301 (t0) cc_final: 0.6285 (p0) REVERT: B 834 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7178 (mt) REVERT: B 964 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8144 (mtpt) REVERT: C 15 CYS cc_start: 0.7130 (m) cc_final: 0.6848 (m) REVERT: C 104 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.8742 (m-90) REVERT: C 190 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7866 (tpt170) REVERT: C 654 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7938 (mt-10) REVERT: C 776 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7834 (ttmt) REVERT: C 834 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7267 (mt) outliers start: 39 outliers final: 19 residues processed: 254 average time/residue: 1.2749 time to fit residues: 384.6074 Evaluate side-chains 255 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 212 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 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 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 776 LYS 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 C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 231 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 296 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 260 optimal weight: 0.2980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099431 restraints weight = 25289.998| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.99 r_work: 0.3122 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 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 = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1720 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= 0.144 Angle : 0.608 12.269 37689 Z= 0.302 Chirality : 0.048 0.671 4416 Planarity : 0.004 0.058 4752 Dihedral : 6.770 57.349 5103 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Rotamer: Outliers : 1.32 % Allowed : 15.24 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.14), residues: 3297 helix: 1.74 (0.19), residues: 690 sheet: 0.28 (0.18), residues: 795 loop : -1.10 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE B 898 TYR 0.019 0.001 TYR B1067 ARG 0.010 0.000 ARG C 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 48) link_NAG-ASN : angle 3.09689 ( 144) link_BETA1-4 : bond 0.00300 ( 12) link_BETA1-4 : angle 3.64546 ( 36) hydrogen bonds : bond 0.04273 ( 1091) hydrogen bonds : angle 5.66136 ( 3009) link_BETA1-6 : bond 0.00203 ( 3) link_BETA1-6 : angle 1.28654 ( 9) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.34493 ( 84) link_BETA1-3 : bond 0.01733 ( 3) link_BETA1-3 : angle 3.37156 ( 9) covalent geometry : bond 0.00327 (27492) covalent geometry : angle 0.56163 (37407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31269.30 seconds wall clock time: 538 minutes 38.89 seconds (32318.89 seconds total)